molecular scale controlled: Topics by Science.gov

Sample records for molecular scale controlled

Shaping the Atomic-Scale Geometries of Electrodes to Control Optical and Electrical Performance of Molecular Devices.

PubMed

Zhao, Zhikai; Liu, Ran; Mayer, Dirk; Coppola, Maristella; Sun, Lu; Kim, Youngsang; Wang, Chuankui; Ni, Lifa; Chen, Xing; Wang, Maoning; Li, Zongliang; Lee, Takhee; Xiang, Dong

2018-04-01

A straightforward method to generate both atomic-scale sharp and atomic-scale planar electrodes is reported. The atomic-scale sharp electrodes are generated by precisely stretching a suspended nanowire, while the atomic-scale planar electrodes are obtained via mechanically controllable interelectrodes compression followed by a thermal-driven atom migration process. Notably, the gap size between the electrodes can be precisely controlled at subangstrom accuracy with this method. These two types of electrodes are subsequently employed to investigate the properties of single molecular junctions. It is found, for the first time, that the conductance of the amine-linked molecular junctions can be enhanced ≈50% as the atomic-scale sharp electrodes are used. However, the atomic-scale planar electrodes show great advantages to enhance the sensitivity of Raman scattering upon the variation of nanogap size. The underlying mechanisms for these two interesting observations are clarified with the help of density functional theory calculation and finite-element method simulation. These findings not only provide a strategy to control the electron transport through the molecule junction, but also pave a way to modulate the optical response as well as to improve the stability of single molecular devices via the rational design of electrodes geometries. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Whole-cell biocomputing

NASA Technical Reports Server (NTRS)

Simpson, M. L.; Sayler, G. S.; Fleming, J. T.; Applegate, B.

2001-01-01

The ability to manipulate systems on the molecular scale naturally leads to speculation about the rational design of molecular-scale machines. Cells might be the ultimate molecular-scale machines and our ability to engineer them is relatively advanced when compared with our ability to control the synthesis and direct the assembly of man-made materials. Indeed, engineered whole cells deployed in biosensors can be considered one of the practical successes of molecular-scale devices. However, these devices explore only a small portion of cellular functionality. Individual cells or self-organized groups of cells perform extremely complex functions that include sensing, communication, navigation, cooperation and even fabrication of synthetic nanoscopic materials. In natural systems, these capabilities are controlled by complex genetic regulatory circuits, which are only partially understood and not readily accessible for use in engineered systems. Here, we focus on efforts to mimic the functionality of man-made information-processing systems within whole cells.
A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device.

PubMed

Lambropoulos, Nicholas A; Reimers, Jeffrey R; Crossley, Maxwell J; Hush, Noel S; Silverbrook, Kia

2013-12-20

A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.
A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device

NASA Astrophysics Data System (ADS)

Lambropoulos, Nicholas A.; Reimers, Jeffrey R.; Crossley, Maxwell J.; Hush, Noel S.; Silverbrook, Kia

2013-12-01

A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.
Synchrotron-based X-ray Fluorescence Microscopy in Conjunction with Nanoindentation to Study Molecular-Scale Interactions of Phenol–Formaldehyde in Wood Cell Walls

Treesearch

Joseph E. Jakes; Christopher G. Hunt; Daniel J. Yelle; Linda Lorenz; Kolby Hirth; Sophie-Charlotte Gleber; Stefan Vogt; Warren Grigsby; Charles R. Frihart

2015-01-01

Understanding and controlling molecular-scale interactions between adhesives and wood polymers are critical to accelerate the development of improved adhesives for advanced wood-based materials. The submicrometer resolution of synchrotron-based X-ray fluorescence microscopy (XFM) was found capable of mapping and quantifying infiltration of Br-labeled phenol−...
A surprising way to control the charge transport in molecular electronics: the subtle impact of the coverage of self-assembled monolayers of floppy molecules adsorbed on metallic electrodes.

PubMed

Bâldea, Ioan

2017-10-26

Inspired by earlier attempts in organic electronics aiming at controlling charge injection from metals into organic materials by manipulating the Schottky energy barrier using self-assembled monolayers (SAMs), recent experimental and theoretical work in molecular electronics showed that metal-organic interfaces can be controlled via changes in the metal work function that are induced by SAMs. In this paper we indicate a different route to achieve interface-driven control over the charge transfer/transport at the molecular scale. It is based on the fact that, in floppy molecule based SAMs, the molecular conformation can be tuned by varying the coverage of the adsorbate. We demonstrate this effect with the aid of benchmark molecules that are often used to fabricate nanojunctions and consist of two rings that can easily rotate relative to each other. We show that, by varying the coverage of the SAM, the twisting angle φ of the considered molecular species can be modified by a factor of two. Given the fact that the low bias conductance G scales as cos 2 φ, this results in a change in G of over one order of magnitude for the considered molecular species. Tuning the twisting angle by controlling the SAM coverage may be significant, e.g., for current efforts to fabricate molecular switches. Conversely, the lack of control over the local SAM coverage may be problematic for the reproducibility and interpretation of the STM (scanning tunneling microscope) measurements on repeatedly forming single molecule break junctions.
Programmable disorder in random DNA tilings

NASA Astrophysics Data System (ADS)

Tikhomirov, Grigory; Petersen, Philip; Qian, Lulu

2017-03-01

Scaling up the complexity and diversity of synthetic molecular structures will require strategies that exploit the inherent stochasticity of molecular systems in a controlled fashion. Here we demonstrate a framework for programming random DNA tilings and show how to control the properties of global patterns through simple, local rules. We constructed three general forms of planar network—random loops, mazes and trees—on the surface of self-assembled DNA origami arrays on the micrometre scale with nanometre resolution. Using simple molecular building blocks and robust experimental conditions, we demonstrate control of a wide range of properties of the random networks, including the branching rules, the growth directions, the proximity between adjacent networks and the size distribution. Much as combinatorial approaches for generating random one-dimensional chains of polymers have been used to revolutionize chemical synthesis and the selection of functional nucleic acids, our strategy extends these principles to random two-dimensional networks of molecules and creates new opportunities for fabricating more complex molecular devices that are organized by DNA nanostructures.
Thermodynamic scaling of dynamics in polymer melts: predictions from the generalized entropy theory.

PubMed

Xu, Wen-Sheng; Freed, Karl F

2013-06-21

Many glass-forming fluids exhibit a remarkable thermodynamic scaling in which dynamic properties, such as the viscosity, the relaxation time, and the diffusion constant, can be described under different thermodynamic conditions in terms of a unique scaling function of the ratio ρ(γ)∕T, where ρ is the density, T is the temperature, and γ is a material dependent constant. Interest in the scaling is also heightened because the exponent γ enters prominently into considerations of the relative contributions to the dynamics from pressure effects (e.g., activation barriers) vs. volume effects (e.g., free volume). Although this scaling is clearly of great practical use, a molecular understanding of the scaling remains elusive. Providing this molecular understanding would greatly enhance the utility of the empirically observed scaling in assisting the rational design of materials by describing how controllable molecular factors, such as monomer structures, interactions, flexibility, etc., influence the scaling exponent γ and, hence, the dynamics. Given the successes of the generalized entropy theory in elucidating the influence of molecular details on the universal properties of glass-forming polymers, this theory is extended here to investigate the thermodynamic scaling in polymer melts. The predictions of theory are in accord with the appearance of thermodynamic scaling for pressures not in excess of ~50 MPa. (The failure at higher pressures arises due to inherent limitations of a lattice model.) In line with arguments relating the magnitude of γ to the steepness of the repulsive part of the intermolecular potential, the abrupt, square-well nature of the lattice model interactions lead, as expected, to much larger values of the scaling exponent. Nevertheless, the theory is employed to study how individual molecular parameters affect the scaling exponent in order to extract a molecular understanding of the information content contained in the exponent. The chain rigidity, cohesive energy, chain length, and the side group length are all found to significantly affect the magnitude of the scaling exponent, and the computed trends agree well with available experiments. The variations of γ with these molecular parameters are explained by establishing a correlation between the computed molecular dependence of the scaling exponent and the fragility. Thus, the efficiency of packing the polymers is established as the universal physical mechanism determining both the fragility and the scaling exponent γ.
NASA Applications of Molecular Nanotechnology

NASA Technical Reports Server (NTRS)

Globus, Al; Bailey, David; Han, Jie; Jaffe, Richard; Levit, Creon; Merkle, Ralph; Srivastava, Deepak

1998-01-01

Laboratories throughout the world are rapidly gaining atomically precise control over matter. As this control extends to an ever wider variety of materials, processes and devices, opportunities for applications relevant to NASA's missions will be created. This document surveys a number of future molecular nanotechnology capabilities of aerospace interest. Computer applications, launch vehicle improvements, and active materials appear to be of particular interest. We also list a number of applications for each of NASA's enterprises. If advanced molecular nanotechnology can be developed, almost all of NASA's endeavors will be radically improved. In particular, a sufficiently advanced molecular nanotechnology can arguably bring large scale space colonization within our grasp.
Multi-scale continuum modeling of biological processes: from molecular electro-diffusion to sub-cellular signaling transduction

NASA Astrophysics Data System (ADS)

Cheng, Y.; Kekenes-Huskey, P.; Hake, J. E.; Holst, M. J.; McCammon, J. A.; Michailova, A. P.

2012-01-01

This paper presents a brief review of multi-scale modeling at the molecular to cellular scale, with new results for heart muscle cells. A finite element-based simulation package (SMOL) was used to investigate the signaling transduction at molecular and sub-cellular scales (http://mccammon.ucsd.edu/smol/, http://FETK.org) by numerical solution of the time-dependent Smoluchowski equations and a reaction-diffusion system. At the molecular scale, SMOL has yielded experimentally validated estimates of the diffusion-limited association rates for the binding of acetylcholine to mouse acetylcholinesterase using crystallographic structural data. The predicted rate constants exhibit increasingly delayed steady-state times, with increasing ionic strength, and demonstrate the role of an enzyme's electrostatic potential in influencing ligand binding. At the sub-cellular scale, an extension of SMOL solves a nonlinear, reaction-diffusion system describing Ca2+ ligand buffering and diffusion in experimentally derived rodent ventricular myocyte geometries. Results reveal the important role of mobile and stationary Ca2+ buffers, including Ca2+ indicator dye. We found that alterations in Ca2+-binding and dissociation rates of troponin C (TnC) and total TnC concentration modulate sub-cellular Ca2+ signals. The model predicts that reduced off-rate in the whole troponin complex (TnC, TnI, TnT) versus reconstructed thin filaments (Tn, Tm, actin) alters cytosolic Ca2+ dynamics under control conditions or in disease-linked TnC mutations. The ultimate goal of these studies is to develop scalable methods and theories for the integration of molecular-scale information into simulations of cellular-scale systems.
Molecular Origins of Mesoscale Ordering in a Metalloamphiphile Phase

PubMed Central

2015-01-01

Controlling the assembly of soft and deformable molecular aggregates into mesoscale structures is essential for understanding and developing a broad range of processes including rare earth extraction and cleaning of water, as well as for developing materials with unique properties. By combined synchrotron small- and wide-angle X-ray scattering with large-scale atomistic molecular dynamics simulations we analyze here a metalloamphiphile–oil solution that organizes on multiple length scales. The molecules associate into aggregates, and aggregates flocculate into meso-ordered phases. Our study demonstrates that dipolar interactions, centered on the amphiphile headgroup, bridge ionic aggregate cores and drive aggregate flocculation. By identifying specific intermolecular interactions that drive mesoscale ordering in solution, we bridge two different length scales that are classically addressed separately. Our results highlight the importance of individual intermolecular interactions in driving mesoscale ordering. PMID:27163014
Tuning the Direction of Intramolecular Charge Transfer and the Nature of the Fluorescent State in a T-Shaped Molecular Dyad.

PubMed

Felouat, Abdellah; D'Aléo, Anthony; Charaf-Eddin, Azzam; Jacquemin, Denis; Le Guennic, Boris; Kim, Eunsun; Lee, Kwang Jin; Woo, Jae Heun; Ribierre, Jean-Charles; Wu, Jeong Weon; Fages, Frédéric

2015-06-18

Controlling photoinduced intramolecular charge transfer at the molecular scale is key to the development of molecular devices for nanooptoelectronics. Here, we describe the design, synthesis, electronic characterization, and photophysical properties of two electron donor-acceptor molecular systems that consist of tolane and BF2-containing curcuminoid chromophoric subunits connected in a T-shaped arrangement. The two π-conjugated segments intersect at the electron acceptor dioxaborine core. From steady-state electronic absorption and fluorescence emission, we find that the photophysics of the dialkylamino-substituted analogue is governed by the occurrence of two closely lying excited states. From DFT calculations, we show that excitation in either of these two states results in a distinct shift of the electron density, whether it occurs along the curcuminoid or tolane moiety. Femtosecond transient absorption spectroscopy confirmed these findings. As a consequence, the nature of the emitting state and the photophysical properties are strongly dependent on solvent polarity. Moreover, these characteristics can also be switched by protonation or complexation at the nitrogen atom of the amino group. These features set new approaches toward the construction of a three-terminal molecular system in which the lateral branch would transduce a change of electronic state and ultimately control charge transport in a molecular-scale device.
Spatially Controlled Noncovalent Functionalization of 2D Materials Based on Molecular Architecture.

PubMed

Bang, Jae Jin; Porter, Ashlin G; Davis, Tyson C; Hayes, Tyler R; Claridge, Shelley A

2018-05-15

Polymerizable amphiphiles can be assembled into lying-down phases on 2D materials such as graphite and graphene to create chemically orthogonal surface patterns at 5-10 nm scales, locally modulating functionality of the 2D basal plane. Functionalization can be carried out through Langmuir-Schaefer conversion, in which a subset of molecules is transferred out of a standing phase film on water onto the 2D substrate. Here, we leverage differences in molecular structure to spatially control transfer at both nanoscopic and microscopic scales. We compare transfer properties of five different single- and dual-chain amphiphiles, demonstrating that those with strong lateral interactions (e.g., hydrogen-bonding networks) exhibit the lowest transfer efficiencies. Since molecular structures also influence microscopic domain morphologies in Langmuir films, we show that it is possible to transfer such microscale patterns, taking advantage of variations in the local transfer rates based on the structural heterogeneity in Langmuir films. Nanoscale domain morphologies also vary in ways that are consistent with predicted relative transfer and diffusion rates. These results suggest strategies to tailor noncovalent functionalization of 2D substrates through controlled LS transfer.
Tip-Enhanced Raman Scattering Microscopy: A Step toward Nanoscale Control of Intrinsic Molecular Properties

NASA Astrophysics Data System (ADS)

Yano, Taka-aki; Hara, Masahiko

2018-06-01

Tip-enhanced Raman scattering microscopy, a family of scanning probe microscopy techniques, has been recognized as a powerful surface analytical technique with both single-molecule sensitivity and angstrom-scale spatial resolution. This review covers the current status of tip-enhanced Raman scattering microscopy in surface and material nanosciences, including a brief history, the basic principles, and applications for the nanoscale characterization of a variety of nanomaterials. The focus is on the recent trend of combining tip-enhanced Raman scattering microscopy with various external stimuli such as pressure, voltage, light, and temperature, which enables the local control of the molecular properties and functions and also enables chemical reactions to be induced on a nanometer scale.
Nanotechnology Presentation Agenda

NASA Technical Reports Server (NTRS)

2005-01-01

Working at the atomic, molecular and supra-molecular levels, in the length scale of approximately 1 - 100 nm range, in order to understand, create and use materials, devices and systems with fundamentally new properties and functions because of their small structure. NNI definition encourages new contributions that were not possible.before. Novel phenomena, properties and functions at nanoscale,which are non scalable outside of the nm domain. The ability to measure / control / manipulate matter at the nanoscale in order to change those properties and functions. Integration along length scales, and fields of application.
Use of 1–4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pang, Yuan-Ping, E-mail: pang@mayo.edu

Highlights: • 1–4 interaction scaling factors are used to adjust conformational energy. • This article reports the effects of these factors on protein conformations. • Reducing these factors changes a helix to a strand in molecular dynamics simulation. • Increasing these factors causes the reverse conformational change. • These factors control the conformational equilibrium between helix and strand. - Abstract: 1–4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6–12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However,more » the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1–4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1–4 interaction scaling factors of protein backbone torsions ϕ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the ϕ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA){sub 3}-NH{sub 2} to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the ϕ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements.« less
An autonomous molecular computer for logical control of gene expression.

PubMed

Benenson, Yaakov; Gil, Binyamin; Ben-Dor, Uri; Adar, Rivka; Shapiro, Ehud

2004-05-27

Early biomolecular computer research focused on laboratory-scale, human-operated computers for complex computational problems. Recently, simple molecular-scale autonomous programmable computers were demonstrated allowing both input and output information to be in molecular form. Such computers, using biological molecules as input data and biologically active molecules as outputs, could produce a system for 'logical' control of biological processes. Here we describe an autonomous biomolecular computer that, at least in vitro, logically analyses the levels of messenger RNA species, and in response produces a molecule capable of affecting levels of gene expression. The computer operates at a concentration of close to a trillion computers per microlitre and consists of three programmable modules: a computation module, that is, a stochastic molecular automaton; an input module, by which specific mRNA levels or point mutations regulate software molecule concentrations, and hence automaton transition probabilities; and an output module, capable of controlled release of a short single-stranded DNA molecule. This approach might be applied in vivo to biochemical sensing, genetic engineering and even medical diagnosis and treatment. As a proof of principle we programmed the computer to identify and analyse mRNA of disease-related genes associated with models of small-cell lung cancer and prostate cancer, and to produce a single-stranded DNA molecule modelled after an anticancer drug.
Organic Single-Crystal Semiconductor Films on a Millimeter Domain Scale.

PubMed

Kwon, Sooncheol; Kim, Jehan; Kim, Geunjin; Yu, Kilho; Jo, Yong-Ryun; Kim, Bong-Joong; Kim, Junghwan; Kang, Hongkyu; Park, Byoungwook; Lee, Kwanghee

2015-11-18

Nucleation and growth processes can be effectively controlled in organic semiconductor films through a new concept of template-mediated molecular crystal seeds during the phase transition; the effective control of these processes ensures millimeter-scale crystal domains, as well as the performance of the resulting organic films with intrinsic hole mobility of 18 cm(2) V(-1) s(-1). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Biological Soft Robotics.

PubMed

Feinberg, Adam W

2015-01-01

In nature, nanometer-scale molecular motors are used to generate force within cells for diverse processes from transcription and transport to muscle contraction. This adaptability and scalability across wide temporal, spatial, and force regimes have spurred the development of biological soft robotic systems that seek to mimic and extend these capabilities. This review describes how molecular motors are hierarchically organized into larger-scale structures in order to provide a basic understanding of how these systems work in nature and the complexity and functionality we hope to replicate in biological soft robotics. These span the subcellular scale to macroscale, and this article focuses on the integration of biological components with synthetic materials, coupled with bioinspired robotic design. Key examples include nanoscale molecular motor-powered actuators, microscale bacteria-controlled devices, and macroscale muscle-powered robots that grasp, walk, and swim. Finally, the current challenges and future opportunities in the field are addressed.
Photo-control of nanointeractions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thomes, William Joseph, Jr.; Potter, Barrett George, Jr.; Jiang, Liu

2005-02-01

The manipulation of physical interactions between structural moieties on the molecular scale is a fundamental hurdle in the realization and operation of nanostructured materials and high surface area microsystem architectures. These include such nano-interaction-based phenomena as self-assembly, fluid flow, and interfacial tribology. The proposed research utilizes photosensitive molecular structures to tune such interactions reversibly. This new material strategy provides optical actuation of nano-interactions impacting behavior on both the nano- and macroscales and with potential to impact directed nanostructure formation, microfluidic rheology, and tribological control.

How molecular epidemiology studies can support the National Malaria Control Program in Papua New Guinea.

PubMed

Koepfli, Cristian; Barry, Alyssa; Javati, Sarah; Timinao, Lincoln; Nate, Elma; Mueller, Ivo; Barnadas, Celine

2014-01-01

Papua New Guinea (PNG) is undertaking intensified efforts to control malaria. The National Malaria Control Program aims to reduce the burden of disease by large-scale distribution of insecticide-treated bednets, improved diagnosis and implementation of new treatments. A scientific program monitoring the effect of these interventions, including molecular epidemiology studies, closely accompanies the program. Laboratory assays have been developed in (or transferred to) PNG to measure prevalence of infection and intensity of transmission as well as potential resistance to currently used drugs. These assays help to assess the impact of the National Malaria Control Program, and they reveal a much clearer picture of malaria epidemiology in PNG. In addition, analysis of the geographical clustering of parasites aids in selecting areas where intensified control will be most successful. This paper gives an overview of current research and recently completed studies in the molecular epidemiology of malaria conducted in Papua New Guinea.
Control of dephasing in rotationally hot molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bartram, David; Ivanov, Misha

We consider a rotationally hot diatomic molecule as an example of an open quantum system, where molecular vibrational wave packets are subject to dephasing due to rovibrational coupling. We report analytical and numerical results addressing whether the dephasing rate can be controlled by adjustment of the initial wave packet phases. It appears that over long time scales, phase-only control is not possible, but for earlier time scales the possibility of phase-only control of dephasing remains. In addition, we point out that the time dependence of the dephasing process depends significantly upon the degeneracy of the rotational environment states.
Transmission of chirality through space and across length scales

NASA Astrophysics Data System (ADS)

Morrow, Sarah M.; Bissette, Andrew J.; Fletcher, Stephen P.

2017-05-01

Chirality is a fundamental property and vital to chemistry, biology, physics and materials science. The ability to use asymmetry to operate molecular-level machines or macroscopically functional devices, or to give novel properties to materials, may address key challenges at the heart of the physical sciences. However, how chirality at one length scale can be translated to asymmetry at a different scale is largely not well understood. In this Review, we discuss systems where chiral information is translated across length scales and through space. A variety of synthetic systems involve the transmission of chiral information between the molecular-, meso- and macroscales. We show how fundamental stereochemical principles may be used to design and understand nanoscale chiral phenomena and highlight important recent advances relevant to nanotechnology. The survey reveals that while the study of stereochemistry on the nanoscale is a rich and dynamic area, our understanding of how to control and harness it and dial-up specific properties is still in its infancy. The long-term goal of controlling nanoscale chirality promises to be an exciting journey, revealing insight into biological mechanisms and providing new technologies based on dynamic physical properties.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Nagaoka, Masataka; Core Research for Evolutional Science and Technology; ESICB, Kyoto University, Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520

A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.
The magnetic field of molecular clouds

NASA Astrophysics Data System (ADS)

Padoan, P.

2018-01-01

The magnetic field of molecular clouds (MCs) plays an important role in the process of star formation: it determines the statistical properties of supersonic turbulence that controls the fragmentation of MCs, controls the angular momentum transport during the protostellar collapse, and affects the stability of circumstellar disks. In this work, we focus on the problem of the determination of the magnetic field strength. We review the idea that the MC turbulence is super-Alfvénic, and we argue that MCs are bound to be born super-Alfvénic. We show that this scenario is supported by results from a recent simulation of supernova-driven turbulence on a scale of 250 pc, where the turbulent cascade is resolved on a wide range of scales, including the interior of MCs.
Live immunization against East Coast fever--current status.

PubMed

Di Giulio, Giuseppe; Lynen, Godelieve; Morzaria, Subhash; Oura, Chris; Bishop, Richard

2009-02-01

The infection-and-treatment method (ITM) for immunization of cattle against East Coast fever has historically been used only on a limited scale because of logistical and policy constraints. Recent large-scale deployment among pastoralists in Tanzania has stimulated demand. Concurrently, a suite of molecular tools, developed from the Theileria parva genome, has enabled improved quality control of the immunizing stabilate and post-immunization monitoring of the efficacy and biological impact of ITM in the field. This article outlines the current status of ITM immunization in the field, with associated developments in the molecular epidemiology of T. parva.
Numerical studies from quantum to macroscopic scales of carbon nanoparticules in hydrogen plasma

NASA Astrophysics Data System (ADS)

Lombardi, Guillaume; Ngandjong, Alain; Mezei, Zsolt; Mougenot, Jonathan; Michau, Armelle; Hassouni, Khaled; Seydou, Mahamadou; Maurel, François

2016-09-01

Dusty plasmas take part in large scientific domains from Universe Science to nanomaterial synthesis processes. They are often generated by growth from molecular precursor. This growth leads to the formation of larger clusters which induce solid germs nucleation. Particle formed are described by an aerosol dynamic taking into account coagulation, molecular deposition and transport processes. These processes are controlled by the elementary particle. So there is a strong coupling between particle dynamics and plasma discharge equilibrium. This study is focused on the development of a multiscale physic and numeric model of hydrogen plasmas and carbon particles around three essential coupled axes to describe the various physical phenomena: (i) Macro/mesoscopic fluid modeling describing in an auto-coherent way, characteristics of the plasma, molecular clusters and aerosol behavior; (ii) the classic molecular dynamics offering a description to the scale molecular of the chains of chemical reactions and the phenomena of aggregation; (iii) the quantum chemistry to establish the activation barriers of the different processes driving the nanopoarticule formation.
Chip-Scale Controlled Storage All-Optical Memory

DTIC Science & Technology

2007-02-01

half width at half maximum KHZ kilo Hertz KK Kramers-Kronig LH light hole MBE molecular beam epitaxy MHz mega Hertz MZI Mach-Zehnder...waveguide geometry. The sample used in experiments 1 and 2 consists of 15 GaAs (135Å)/Al0.3Ga0.7As(150 Å) QWs grown by molecular beam epitaxy (MBE...We developed the capability to grow GaAs QWs on (110)-oriented substrates using molecular beam epitaxy in a very short amount of time. The very
An autonomous molecular computer for logical control of gene expression

PubMed Central

Benenson, Yaakov; Gil, Binyamin; Ben-Dor, Uri; Adar, Rivka; Shapiro, Ehud

2013-01-01

Early biomolecular computer research focused on laboratory-scale, human-operated computers for complex computational problems1–7. Recently, simple molecular-scale autonomous programmable computers were demonstrated8–15 allowing both input and output information to be in molecular form. Such computers, using biological molecules as input data and biologically active molecules as outputs, could produce a system for ‘logical’ control of biological processes. Here we describe an autonomous biomolecular computer that, at least in vitro, logically analyses the levels of messenger RNA species, and in response produces a molecule capable of affecting levels of gene expression. The computer operates at a concentration of close to a trillion computers per microlitre and consists of three programmable modules: a computation module, that is, a stochastic molecular automaton12–17; an input module, by which specific mRNA levels or point mutations regulate software molecule concentrations, and hence automaton transition probabilities; and an output module, capable of controlled release of a short single-stranded DNA molecule. This approach might be applied in vivo to biochemical sensing, genetic engineering and even medical diagnosis and treatment. As a proof of principle we programmed the computer to identify and analyse mRNA of disease-related genes18–22 associated with models of small-cell lung cancer and prostate cancer, and to produce a single-stranded DNA molecule modelled after an anticancer drug. PMID:15116117
Molecular inversion probe assay.

PubMed

Absalan, Farnaz; Ronaghi, Mostafa

2007-01-01

We have described molecular inversion probe technologies for large-scale genetic analyses. This technique provides a comprehensive and powerful tool for the analysis of genetic variation and enables affordable, large-scale studies that will help uncover the genetic basis of complex disease and explain the individual variation in response to therapeutics. Major applications of the molecular inversion probes (MIP) technologies include targeted genotyping from focused regions to whole-genome studies, and allele quantification of genomic rearrangements. The MIP technology (used in the HapMap project) provides an efficient, scalable, and affordable way to score polymorphisms in case/control populations for genetic studies. The MIP technology provides the highest commercially available multiplexing levels and assay conversion rates for targeted genotyping. This enables more informative, genome-wide studies with either the functional (direct detection) approach or the indirect detection approach.
Ultrafast optics. Ultrafast optical control by few photons in engineered fiber.

PubMed

Nissim, R; Pejkic, A; Myslivets, E; Kuo, B P; Alic, N; Radic, S

2014-07-25

Fast control of a strong optical beam by a few photons is an outstanding challenge that limits the performance of quantum sensors and optical processing devices. We report that a fast and efficient optical gate can be realized in an optical fiber that has been engineered with molecular-scale accuracy. Highly efficient, distributed phase-matched photon-photon interaction was achieved in the fiber with locally controlled, nanometer-scale core variations. A three-photon input was used to manipulate a Watt-scale beam at a speed exceeding 500 gigahertz. In addition to very fast beam control, the results provide a path to developing a new class of sensitive receivers capable of operating at very high rates. Copyright © 2014, American Association for the Advancement of Science.
Supramolecular Systems and Chemical Reactions in Single-Molecule Break Junctions.

PubMed

Li, Xiaohui; Hu, Duan; Tan, Zhibing; Bai, Jie; Xiao, Zongyuan; Yang, Yang; Shi, Jia; Hong, Wenjing

2017-04-01

The major challenges of molecular electronics are the understanding and manipulation of the electron transport through the single-molecule junction. With the single-molecule break junction techniques, including scanning tunneling microscope break junction technique and mechanically controllable break junction technique, the charge transport through various single-molecule and supramolecular junctions has been studied during the dynamic fabrication and continuous characterization of molecular junctions. This review starts from the charge transport characterization of supramolecular junctions through a variety of noncovalent interactions, such as hydrogen bond, π-π interaction, and electrostatic force. We further review the recent progress in constructing highly conductive molecular junctions via chemical reactions, the response of molecular junctions to external stimuli, as well as the application of break junction techniques in controlling and monitoring chemical reactions in situ. We suggest that beyond the measurement of single molecular conductance, the single-molecule break junction techniques provide a promising access to study molecular assembly and chemical reactions at the single-molecule scale.
Liquid crystal templating as an approach to spatially and temporally organise soft matter.

PubMed

van der Asdonk, Pim; Kouwer, Paul H J

2017-10-02

Chemistry quickly moves from a molecular science to a systems science. This requires spatial and temporal control over the organisation of molecules and molecular assemblies. Whilst Nature almost by default (transiently) organises her components at multiple different length scales, scientists struggle to realise even relatively straightforward patterns. In the past decades, supramolecular chemistry has taught us the rules to precisely engineer molecular assembly at the nanometre scale. At higher length scales, however, we are bound to top-down nanotechnology techniques to realise order. For soft, biological matter, many of these top-down techniques come with serious limitations since the molecules generally show low susceptibilities to the applied stimuli. A new method is based on liquid crystal templating. In this hierarchical approach, a liquid crystalline host serves as the scaffold to order polymers or assemblies. Being a liquid crystal, the host material can be ordered at many different length scales and on top of that, is highly susceptible to many external stimuli, which can even be used to manipulate the liquid crystal organisation in time. As a result, we anticipate large control over the organisation of the materials inside the liquid crystalline host. Recently, liquid crystal templating was also realised in water. This suddenly makes this tool highly applicable to start organising more delicate biological materials or even small organisms. We review the scope and limitations of liquid crystal templating and look out to where the technique may lead us.
LAMMPS strong scaling performance optimization on Blue Gene/Q

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coffman, Paul; Jiang, Wei; Romero, Nichols A.

2014-11-12

LAMMPS "Large-scale Atomic/Molecular Massively Parallel Simulator" is an open-source molecular dynamics package from Sandia National Laboratories. Significant performance improvements in strong-scaling and time-to-solution for this application on IBM's Blue Gene/Q have been achieved through computational optimizations of the OpenMP versions of the short-range Lennard-Jones term of the CHARMM force field and the long-range Coulombic interaction implemented with the PPPM (particle-particle-particle mesh) algorithm, enhanced by runtime parameter settings controlling thread utilization. Additionally, MPI communication performance improvements were made to the PPPM calculation by re-engineering the parallel 3D FFT to use MPICH collectives instead of point-to-point. Performance testing was done using anmore » 8.4-million atom simulation scaling up to 16 racks on the Mira system at Argonne Leadership Computing Facility (ALCF). Speedups resulting from this effort were in some cases over 2x.« less
Light induced kickoff of magnetic domain walls in Ising chains

NASA Astrophysics Data System (ADS)

Bogani, Lapo

2012-02-01

Controlling the speed at which systems evolve is a challenge shared by all disciplines, and otherwise unrelated areas use common theoretical frameworks towards this goal. A particularly widespread model is Glauber dynamics, which describes the time evolution of the Ising model and can be applied to any binary system. Here we show, using molecular nanowires under irradiation, that Glauber dynamics can be controlled by a novel domain-wall kickoff mechanism. Contrary to known processes, the kickoff has unambiguous fingerprints, slowing down the spin-flip attempt rate by several orders of magnitude, and following a scaling law. The required irradiation power is very low, a substantial improvement over present methods of magnetooptical switching: in our experimental demonstration we switched molecular nanowires with light, using powers thousands of times lower than in previous optical switching methods. This manipulation of stochastic dynamic processes is extremely clean, leading to fingerprint signatures and scaling laws. These observations can be used, in material science, to better study domain-wall displacements and solitons in discrete lattices. These results provide a new way to control and study stochastic dynamic processes. Being general for Glauber dynamics, they can be extended to different kinds of magnetic nanowires and to a myriad of fields, ranging from social evolution to neural networks and chemical reactivity. For nanoelectronics and molecular spintronics the kickoff affords external control of molecular spin-valves and a magnetic fingerprint in single molecule measurements. It can also be applied to the dynamics of mechanical switches and the related study of phasons and order-disorder transitions.
A facile single-step synthesis of polyvinylpyrrolidone-silver nanocomposites using a conventional spray dryer

NASA Astrophysics Data System (ADS)

Kim, Byung-Ho; Hyuck Kim, Yoon; Lee, Young Jin; Lee, Mi Jai; Kim, Jin-Ho; Hwang, Jonghee; Jeon, Dae-Woo

2018-01-01

We have developed a facile single-step synthesis of silver nanocomposite using a conventional spray dryer. We investigated the synthetic conditions by controlling the concentrations of the chemical reactants. Further, we confirmed the effect of the molecular weight of polyvinylpyrrolidones, and revealed that the molecular weight significantly affected the properties of the resultant silver nanocomposites. The long-term stability of the silver nanocomposites was tested, and little change was observed, even after storage for three months. Most of all, the simple commercial implementation, in combination with large-scale synthesis, possesses a variety of advantages, compared to conventional complicated and costly dry-process synthesis methods. Thus, our method presents opportunities for further investigation, for both lab-scale studies and large-scale industrial applications.
Redox control of molecular motion in switchable artificial nanoscale devices.

PubMed

Credi, Alberto; Semeraro, Monica; Silvi, Serena; Venturi, Margherita

2011-03-15

The design, synthesis, and operation of molecular-scale systems that exhibit controllable motions of their component parts is a topic of great interest in nanoscience and a fascinating challenge of nanotechnology. The development of this kind of species constitutes the premise to the construction of molecular machines and motors, which in a not-too-distant future could find applications in fields such as materials science, information technology, energy conversion, diagnostics, and medicine. In the past 25 years the development of supramolecular chemistry has enabled the construction of an interesting variety of artificial molecular machines. These devices operate via electronic and molecular rearrangements and, like the macroscopic counterparts, they need energy to work as well as signals to communicate with the operator. Here we outline the design principles at the basis of redox switching of molecular motion in artificial nanodevices. Redox processes, chemically, electrically, or photochemically induced, can indeed supply the energy to bring about molecular motions. Moreover, in the case of electrically and photochemically induced processes, electrochemical and photochemical techniques can be used to read the state of the system, and thus to control and monitor the operation of the device. Some selected examples are also reported to describe the most representative achievements in this research area.
Tuning charge and correlation effects for a single molecule on a graphene device

DOE PAGES

Wickenburg, Sebastian; Lu, Jiong; Lischner, Johannes; ...

2016-11-25

The ability to understand and control the electronic properties of individual molecules in a device environment is crucial for developing future technologies at the nanometre scale and below. Achieving this, however, requires the creation of three-terminal devices that allow single molecules to be both gated and imaged at the atomic scale. We have accomplished this by integrating a graphene field effect transistor with a scanning tunnelling microscope, thus allowing gate-controlled charging and spectroscopic interrogation of individual tetrafluoro-tetracyanoquinodimethane molecules. We observe a non-rigid shift in the molecule’s lowest unoccupied molecular orbital energy (relative to the Dirac point) as a function ofmore » gate voltage due to graphene polarization effects. Our results show that electron–electron interactions play an important role in how molecular energy levels align to the graphene Dirac point, and may significantly influence charge transport through individual molecules incorporated in graphene-based nanodevices.« less
Exciton dynamics of C60-based single-photon emitters explored by Hanbury Brown-Twiss scanning tunnelling microscopy.

PubMed

Merino, P; Große, C; Rosławska, A; Kuhnke, K; Kern, K

2015-09-29

Exciton creation and annihilation by charges are crucial processes for technologies relying on charge-exciton-photon conversion. Improvement of organic light sources or dye-sensitized solar cells requires methods to address exciton dynamics at the molecular scale. Near-field techniques have been instrumental for this purpose; however, characterizing exciton recombination with molecular resolution remained a challenge. Here, we study exciton dynamics by using scanning tunnelling microscopy to inject current with sub-molecular precision and Hanbury Brown-Twiss interferometry to measure photon correlations in the far-field electroluminescence. Controlled injection allows us to generate excitons in solid C60 and let them interact with charges during their lifetime. We demonstrate electrically driven single-photon emission from localized structural defects and determine exciton lifetimes in the picosecond range. Monitoring lifetime shortening and luminescence saturation for increasing carrier injection rates provides access to charge-exciton annihilation dynamics. Our approach introduces a unique way to study single quasi-particle dynamics on the ultimate molecular scale.
Comparison of single-ion molecular dynamics in common solvents

NASA Astrophysics Data System (ADS)

Muralidharan, A.; Pratt, L. R.; Chaudhari, M. I.; Rempe, S. B.

2018-06-01

Laying a basis for molecularly specific theory for the mobilities of ions in solutions of practical interest, we report a broad survey of velocity autocorrelation functions (VACFs) of Li+ and PF6- ions in water, ethylene carbonate, propylene carbonate, and acetonitrile solutions. We extract the memory function, γ(t), which characterizes the random forces governing the mobilities of ions. We provide comparisons controlling for the effects of electrolyte concentration and ion-pairing, van der Waals attractive interactions, and solvent molecular characteristics. For the heavier ion (PF6-), velocity relaxations are all similar: negative tail relaxations for the VACF and a clear second relaxation for γ (t ), observed previously also for other molecular ions and with n-pentanol as the solvent. For the light Li+ ion, short time-scale oscillatory behavior masks simple, longer time-scale relaxation of γ (t ). But the corresponding analysis of the solventberg Li+(H2O)4 does conform to the standard picture set by all the PF6- results.

Molecular-Scale Structural Controls on Nanoscale Growth Processes: Step-Specific Regulation of Biomineral Morphology

NASA Astrophysics Data System (ADS)

Dove, P. M.; Davis, K. J.; De Yoreo, J. J.; Orme, C. A.

2001-12-01

Deciphering the complex strategies by which organisms produce nanocrystalline materials with exquisite morphologies is central to understanding biomineralizing systems. One control on the morphology of biogenic nanoparticles is the specific interactions of their surfaces with the organic functional groups provided by the organism and the various inorganic species present in the ambient environment. It is now possible to directly probe the microscopic structural controls on crystal morphology by making quantitative measurements of the dynamic processes occurring at the mineral-water interface. These observations can provide crucial information concerning the actual mechanisms of growth that is otherwise unobtainable through macroscopic techniques. Here we use in situ molecular-scale observations of step dynamics and growth hillock morphology to directly resolve roles of principal impurities in regulating calcite surface morphologies. We show that the interactions of certain inorganic as well as organic impurities with the calcite surface are dependent upon the molecular-scale structures of step-edges. These interactions can assume a primary role in directing crystal morphology. In calcite growth experiments containing magnesium, we show that growth hillock structures become modified owing to the preferential inhibition of step motion along directions approximately parallel to the [010]. Compositional analyses have shown that Mg incorporates at different levels into the two types of nonequivalent steps, which meet at the hillock corner parallel to [010]. A simple calculation of the strain caused by this difference indicates that we should expect a significant retardation at this corner, in agreement with the observed development of [010] steps. If the low-energy step-risers produced by these [010] steps is perpendicular to the c-axis as seems likely from crystallographic considerations, this effect provides a plausible mechanism for the elongated calcite crystal habits found in natural environments that contain magnesium. In a separate study, step-specific interactions are also found between chiral aspartate molecules and the calcite surface. The L and D- aspartate enantiomers exhibit structure preferences for the different types of step-risers on the calcite surface. These site-specific interactions result in the transfer of asymmetry from the organic molecule to the crystal surface through the formation of chiral growth hillocks and surface morphologies. These studies yield direct experimental insight into the molecular-scale structural controls on nanocrystal morphology in biomineralizing systems.
Mineral transformation controls speciation and pore-fluid transmission of contaminants in waste-weathered Hanford sediments

NASA Astrophysics Data System (ADS)

Perdrial, Nicolas; Thompson, Aaron; O'Day, Peggy A.; Steefel, Carl I.; Chorover, Jon

2014-09-01

Portions of the Hanford Site (WA, USA) vadose zone were subjected to weathering by caustic solutions during documented releases of high level radioactive waste (containing Sr, Cs and I) from leaking underground storage tanks. Previous studies have shown that waste-sediment interactions can promote variable incorporation of contaminants into neo-formed mineral products (including feldspathoids and zeolites), but processes regulating the subsequent contaminant release from these phases into infiltrating background pore waters remain poorly known. In this paper, reactive transport experiments were conducted with Hanford sediments previously weathered for one year in simulated hyper-alkaline waste solutions containing high or low 88Sr, 127I, and 133Cs concentrations, with or without CO2(aq). These waste-weathered sediments were leached in flow-through column experiments with simulated background pore water (characteristic of meteoric recharge) to measure contaminant release from solids formed during waste-sediment interaction. Contaminant sorption-desorption kinetics and mineral transformation reactions were both monitored using continuous-flow and wet-dry cycling regimes for ca. 300 pore volumes. Less than 20% of contaminant 133Cs and 88Sr mass and less than 40% 127I mass were released over the course of the experiment. To elucidate molecular processes limiting contaminant release, reacted sediments were studied with micro- (TEM and XRD) and molecular- (Sr K-edge EXAFS) scale methods. Contaminant dynamics in column experiments were principally controlled by rapid dissolution of labile solids and competitive exchange reactions. In initially feldspathoidic systems, time-dependent changes in the local zeolitic bonding environment observed with X-ray diffraction and EXAFS are responsible for limiting contaminant release. Linear combination fits and shell-by-shell analysis of Sr K-edge EXAFS data revealed modification in Sr-Si/Al distances within the zeolite cage. Wet-dry cycling did not affect significantly molecular-scale transformations relative to continuous-flow controls. Results indicate that contaminants bound to the solid phase in distinct micro- and molecular-scale coordinative environments can generate similar macro-scale release behaviors, highlighting the need for multi-scale interrogations to constrain mechanisms of reactive transport. Data also indicate that weathering-induced change in ion exchange selectivity coefficients should be incorporated in simulations of contaminant release from caustic high-level radioactive waste impacted sediments.
Molecular dynamics modeling of bonding two materials by atomic scale friction stir welding at different process parameters

NASA Astrophysics Data System (ADS)

Konovalenko S., Iv.; Psakhie, S. G.

2017-12-01

Using the molecular dynamics method, we simulated the atomic scale butt friction stir welding on two crystallites and varied the onset FSW tool plunge depth. The effects of the plunge depth value on the thermomechanical evolution of nanosized crystallites and mass transfer in the course of FSW have been studied. The increase of plunge depth values resulted in more intense heating and reducing the plasticized metal resistance to the tool movement. The mass transfer intensity was hardly dependent on the plunge depth value. The plunge depth was recommended to be used as a FSW process control parameter in addition to the commonly used ones.
Excited state dynamics & optical control of molecular motors

NASA Astrophysics Data System (ADS)

Wiley, Ted; Sension, Roseanne

2014-03-01

Chiral overcrowded alkenes are likely candidates for light driven rotary molecular motors. At their core, these molecular motors are based on the chromophore stilbene, undergoing ultrafast cis/trans photoisomerization about their central double bond. Unlike stilbene, the photochemistry of molecular motors proceeds in one direction only. This unidirectional rotation is a result of helicity in the molecule induced by steric hindrance. However, the steric hindrance which ensures unidirectional excited state rotation, has the unfortunate consequence of producing large ground state barriers which dramatically decrease the overall rate of rotation. These molecular scale ultrafast motors have only recently been studied by ultrafast spectroscopy. Our lab has studied the photochemistry and photophysics of a ``first generation'' molecular motor with UV-visible transient absorption spectroscopy. We hope to use optical pulse shaping to enhance the efficiency and turnover rate of these molecular motors.
Massively Parallel, Molecular Analysis Platform Developed Using a CMOS Integrated Circuit With Biological Nanopores

PubMed Central

Roever, Stefan

2012-01-01

A massively parallel, low cost molecular analysis platform will dramatically change the nature of protein, molecular and genomics research, DNA sequencing, and ultimately, molecular diagnostics. An integrated circuit (IC) with 264 sensors was fabricated using standard CMOS semiconductor processing technology. Each of these sensors is individually controlled with precision analog circuitry and is capable of single molecule measurements. Under electronic and software control, the IC was used to demonstrate the feasibility of creating and detecting lipid bilayers and biological nanopores using wild type α-hemolysin. The ability to dynamically create bilayers over each of the sensors will greatly accelerate pore development and pore mutation analysis. In addition, the noise performance of the IC was measured to be 30fA(rms). With this noise performance, single base detection of DNA was demonstrated using α-hemolysin. The data shows that a single molecule, electrical detection platform using biological nanopores can be operationalized and can ultimately scale to millions of sensors. Such a massively parallel platform will revolutionize molecular analysis and will completely change the field of molecular diagnostics in the future.
A concurrent multiscale micromorphic molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Shaofan, E-mail: shaofan@berkeley.edu; Tong, Qi

2015-04-21

In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from firstmore » principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation.« less
Belowground Carbon Cycling Processes at the Molecular Scale: An EMSL Science Theme Advisory Panel Workshop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hess, Nancy J.; Brown, Gordon E.; Plata, Charity

2014-02-21

As part of the Belowground Carbon Cycling Processes at the Molecular Scale workshop, an EMSL Science Theme Advisory Panel meeting held in February 2013, attendees discussed critical biogeochemical processes that regulate carbon cycling in soil. The meeting attendees determined that as a national scientific user facility, EMSL can provide the tools and expertise needed to elucidate the molecular foundation that underlies mechanistic descriptions of biogeochemical processes that control carbon allocation and fluxes at the terrestrial/atmospheric interface in landscape and regional climate models. Consequently, the workshop's goal was to identify the science gaps that hinder either development of mechanistic description ofmore » critical processes or their accurate representation in climate models. In part, this report offers recommendations for future EMSL activities in this research area. The workshop was co-chaired by Dr. Nancy Hess (EMSL) and Dr. Gordon Brown (Stanford University).« less
DOE Office of Scientific and Technical Information (OSTI.GOV)

Bolmatov, Dima; Zhernenkov, Mikhail; Zav’yalov, Dmitry

Here in this work we report on terahertz phononic excitations in 2D gold nanoparticle arrays in a water matrix through a series of large-scale molecular dynamics simulations. For the first time, we observe acoustic Dirac-like crossings in H (H 2O) atomic (molecular) networks which emerge due to an intraband phononic scattering. These crossings are the phononic fingerprints of ice-like arrangements of H (H 2O) atomic (molecular) networks at nanometer scale. We reveal how phononic excitations in metallic nanoparticles and the water matrix reciprocally impact on one another providing the mechanism for the THz phononics manipulation via structural engineering. In addition,more » we show that by tuning the arrangement of 2D gold nanoparticle assemblies the Au phononic polarizations experience sub-terahertz hybridization (Kohn anomaly) due to surface electron-phonon relaxation processes. This opens the way for the sound control and manipulation in soft matter metamaterials at nanoscale.« less
Physiological controls of large‐scale patterning in planarian regeneration: a molecular and computational perspective on growth and form

PubMed Central

Durant, Fallon; Lobo, Daniel; Hammelman, Jennifer

2016-01-01

Abstract Planaria are complex metazoans that repair damage to their bodies and cease remodeling when a correct anatomy has been achieved. This model system offers a unique opportunity to understand how large‐scale anatomical homeostasis emerges from the activities of individual cells. Much progress has been made on the molecular genetics of stem cell activity in planaria. However, recent data also indicate that the global pattern is regulated by physiological circuits composed of ionic and neurotransmitter signaling. Here, we overview the multi‐scale problem of understanding pattern regulation in planaria, with specific focus on bioelectric signaling via ion channels and gap junctions (electrical synapses), and computational efforts to extract explanatory models from functional and molecular data on regeneration. We present a perspective that interprets results in this fascinating field using concepts from dynamical systems theory and computational neuroscience. Serving as a tractable nexus between genetic, physiological, and computational approaches to pattern regulation, planarian pattern homeostasis harbors many deep insights for regenerative medicine, evolutionary biology, and engineering. PMID:27499881
Ribosomes are optimized for autocatalytic production

NASA Astrophysics Data System (ADS)

Reuveni, Shlomi; Ehrenberg, Måns; Paulsson, Johan

2017-07-01

Many fine-scale features of ribosomes have been explained in terms of function, revealing a molecular machine that is optimized for error-correction, speed and control. Here we demonstrate mathematically that many less well understood, larger-scale features of ribosomes—such as why a few ribosomal RNA molecules dominate the mass and why the ribosomal protein content is divided into 55-80 small, similarly sized segments—speed up their autocatalytic production.
Competition of mesoscales and crossover to theta-point tricriticality in near-critical polymer solutions.

PubMed

Anisimov, M A; Kostko, A F; Sengers, J V; Yudin, I K

2005-10-22

The approach to asymptotic critical behavior in polymer solutions is governed by a competition between the correlation length of critical fluctuations diverging at the critical point of phase separation and an additional mesoscopic length scale, the radius of gyration. In this paper we present a theory for crossover between two universal regimes: a regime with Ising (fluctuation-induced) asymptotic critical behavior, where the correlation length prevails, and a mean-field tricritical regime with theta-point behavior controlled by the mesoscopic polymer chain. The theory yields a universal scaled description of existing experimental phase-equilibria data and is in excellent agreement with our light-scattering experiments on polystyrene solutions in cyclohexane with polymer molecular weights ranging from 2 x 10(5) up to 11.4 x 10(6). The experiments demonstrate unambiguously that crossover to theta-point tricriticality is controlled by a competition of the two mesoscales. The critical amplitudes deduced from our experiments depend on the polymer molecular weight as predicted by de Gennes [Phys. Lett. 26A, 313 (1968)]. Experimental evidence for the presence of logarithmic corrections to mean-field tricritical theta-point behavior in the molecular-weight dependence of the critical parameters is also presented.
Mesoporous Polymer Frameworks from End-Reactive Bottlebrush Copolymers

DOE PAGES

Altay, Esra; Nykypanchuk, Dmytro; Rzayev, Javid

2017-08-07

Reticulated nanoporous materials generated by versatile molecular framework approaches are limited to pore dimensions on the scale of the utilized rigid molecular building blocks (<5 nm). The inherent flexibility of linear polymers precludes their utilization as long framework connectors for the extension of this strategy to larger length scales. We report a method for the fabrication of mesoporous frameworks by using bottlebrush copolymers with reactive end blocks serving as rigid macromolecular interconnectors with directional reactivity. End-reactive bottlebrush copolymers with pendant alkene functionalities were synthesized by a combination of controlled radical polymerization and polymer modification protocols. Ru-catalyzed cross-metathesis cross-linking of bottlebrushmore » copolymers with two reactive end blocks resulted in the formation of polymer frameworks where isolated cross-linked domains were interconnected with bottlebrush copolymer bridges. The resulting materials were characterized by a continuous network pore structure with average pore sizes of 9–50 nm, conveniently tunable by the length of the utilized bottlebrush copolymer building blocks. As a result, the materials fabrication strategy described in this work expands the length scale of molecular framework materials and provides access to mesoporous polymers with a molecularly tunable reticulated pore structure without the need for templating, sacrificial component etching, or supercritical fluid drying.« less
Nanolithographic control of the spatial organization of cellular adhesion receptors at the single-molecule level

PubMed Central

Schvartzman, Mark; Palma, Matteo; Sable, Julia; Abramson, Justin; Hu, Xian; Sheetz, Michael P.; Wind, Shalom J.

2011-01-01

The ability to control the placement of individual molecules promises to enable a wide range of applications and is a key challenge in nanoscience and nanotechnology. Many biological interactions, in particular, are sensitive to the precise geometric arrangement of proteins. We have developed a technique which combines molecular-scale nanolithography with site-selective biochemistry to create biomimetic arrays of individual protein binding sites. The binding sites can be arranged in heterogeneous patterns of virtually any possible geometry with a nearly unlimited number of degrees of freedom. We have used these arrays to explore how the geometric organization of the extracellular matrix (ECM) binding ligand RGD (Arg-Gly-Asp) affects cell adhesion and spreading. Systematic variation of spacing, density and cluster size of individual integrin binding sites was used to elicit different cell behavior. Cell spreading assays on arrays of different geometric arrangements revealed a dramatic increase in spreading efficiency when at least 4 liganded sites were spaced within 60 nm or less, with no dependence on global density. This points to the existence of a minimal matrix adhesion unit for fibronectin defined in space and stoichiometry. Developing an understanding of the ECM geometries that activate specific cellular functional complexes is a critical step toward controlling cell behavior. Potential practical applications range from new therapeutic treatments to the rational design of tissue scaffolds that can optimize healing without scarring. More broadly, spatial control at the single-molecule level can elucidate factors controlling individual molecular interactions and can enable synthesis of new systems based on molecular-scale architectures. PMID:21319842
Can mechanics control pattern formation in plants?

PubMed

Dumais, Jacques

2007-02-01

Development of the plant body entails many pattern forming events at scales ranging from the cellular level to the whole plant. Recent evidence suggests that mechanical forces play a role in establishing some of these patterns. The development of cellular configurations in glandular trichomes and the rippling of leaf surfaces are discussed in depth to illustrate how intricate patterns can emerge from simple and well-established molecular and cellular processes. The ability of plants to sense and transduce mechanical signals suggests that complex interactions between mechanics and chemistry are possible during plant development. The inclusion of mechanics alongside traditional molecular controls offers a more comprehensive view of developmental processes.
Controlling electron localization in H2 + by intense plasmon-enhanced laser fields

NASA Astrophysics Data System (ADS)

Yavuz, I.; Ciappina, M. F.; Chacón, A.; Altun, Z.; Kling, M. F.; Lewenstein, M.

2016-03-01

We present a theoretical study of the H2 + molecular ion wave-packet dynamics in plasmon-enhanced laser fields. These fields may be produced, for instance, when metallic nanostructures are illuminated by a laser pulse of moderated intensity. Their main property is that they vary in space on a nanometric scale. We demonstrate that the spatial inhomogeneous character of the plasmonic fields leads to an enhancement of electron localization (EL), an instrumental phenomenon to control molecular fragmentation. We suggest that the charge imbalance induced by the surface-plasmon resonance near the metallic nanostructure is the origin of the increase in the EL.
Self-assembly patterning of organic molecules on a surface

DOEpatents

Pan, Minghu; Fuentes-Cabrera, Miguel; Maksymovych, Petro; Sumpter, Bobby G.; Li, Qing

2017-04-04

The embodiments disclosed herein include all-electron control over a chemical attachment and the subsequent self-assembly of an organic molecule into a well-ordered three-dimensional monolayer on a metal surface. The ordering or assembly of the organic molecule may be through electron excitation. Hot-electron and hot-hole excitation enables tethering of the organic molecule to a metal substrate, such as an alkyne group to a gold surface. All-electron reactions may allow a direct control over the size and shape of the self-assembly, defect structures and the reverse process of molecular disassembly from single molecular level to mesoscopic scale.
Mass Spectrometry as a Preparative Tool for the Surface Science of Large Molecules

NASA Astrophysics Data System (ADS)

Rauschenbach, Stephan; Ternes, Markus; Harnau, Ludger; Kern, Klaus

2016-06-01

Measuring and understanding the complexity that arises when nanostructures interact with their environment are one of the major current challenges of nanoscale science and technology. High-resolution microscopy methods such as scanning probe microscopy have the capacity to investigate nanoscale systems with ultimate precision, for which, however, atomic scale precise preparation methods of surface science are a necessity. Preparative mass spectrometry (pMS), defined as the controlled deposition of m/z filtered ion beams, with soft ionization sources links the world of large, biological molecules and surface science, enabling atomic scale chemical control of molecular deposition in ultrahigh vacuum (UHV). Here we explore the application of high-resolution scanning probe microscopy and spectroscopy to the characterization of structure and properties of large molecules. We introduce the fundamental principles of the combined experiments electrospray ion beam deposition and scanning tunneling microscopy. Examples for the deposition and investigation of single particles, for layer and film growth, and for the investigation of electronic properties of individual nonvolatile molecules show that state-of-the-art pMS technology provides a platform analog to thermal evaporation in conventional molecular beam epitaxy. Additionally, it offers additional, unique features due to the use of charged polyatomic particles. This new field is an enormous sandbox for novel molecular materials research and demands the development of advanced molecular ion beam technology.
'Next-Generation' Surveillance: An Epidemiologists' Perspective on the Use of Molecular Information in Food Safety and Animal Health Decision-Making.

PubMed

Muellner, P; Stärk, K D C; Dufour, S; Zadoks, R N

2016-08-01

Advances in the availability and affordability of molecular and genomic data are transforming human health care. Surveillance aimed at supporting and improving food safety and animal health is likely to undergo a similar transformation. We propose a definition of 'molecular surveillance' in this context and argue that molecular data are an adjunct to rather than a substitute for sound epidemiological study and surveillance design. Specific considerations with regard to sample collection are raised, as is the importance of the relation between the molecular clock speed of genetic markers and the spatiotemporal scale of the surveillance activity, which can be control- or strategy-focused. Development of standards for study design and assessment of molecular surveillance system attributes is needed, together with development of an interdisciplinary skills base covering both molecular and epidemiological principles. © 2015 Blackwell Verlag GmbH.
Atomic and molecular dynamics triggered by ultrashort light pulses on the atto- to picosecond time scale

NASA Astrophysics Data System (ADS)

Pabst, Stefan

2013-04-01

Time-resolved investigations of ultrafast electronic and molecular dynamics were not possible until recently. The typical time scale of these processes is in the picosecond to attosecond realm. The tremendous technological progress in recent years made it possible to generate ultrashort pulses, which can be used to trigger, to watch, and to control atomic and molecular motion. This tutorial focuses on experimental and theoretical advances which are used to study the dynamics of electrons and molecules in the presence of ultrashort pulses. In the first part, the rotational dynamics of molecules, which happens on picosecond and femtosecond time scales, is reviewed. Well-aligned molecules are particularly suitable for angle-dependent investigations like x-ray diffraction or strong-field ionization experiments. In the second part, the ionization dynamics of atoms is studied. The characteristic time scale lies, here, in the attosecond to few-femtosecond regime. Although a one-particle picture has been successfully applied to many processes, many-body effects do constantly occur. After a broad overview of the main mechanisms and the most common tools in attosecond physics, examples of many-body dynamics in the attosecond world (e.g., in high-harmonic generation and attosecond transient absorption spectroscopy) are discussed.
Molecular dynamics modeling of bonding two materials by atomic scale friction stir welding

NASA Astrophysics Data System (ADS)

Konovalenko S., Iv.; Konovalenko, Ig. S.; Psakhie, S. G.

2017-12-01

Molecular dynamics model of atomic scale friction stir welding has been developed. Formation of a butt joint between two crystallites was modeled by means of rotating rigid conical tool traveling along the butt joint line. The formed joint had an intermixed atomic structure composed of atoms initially belonged to the opposite mated piece of metal. Heat removal was modeled by adding the extra viscous force to peripheral atomic layers. This technique provides the temperature control in the tool-affected zone during welding. Auxiliary vibration action was added to the rotating tool. The model provides the variation of the tool's angular velocity, amplitude, frequency and direction of the auxiliary vibration action to provide modeling different welding modes.

Molecular Velcro constructed from polymer loop brushes showing enhanced adhesion force

NASA Astrophysics Data System (ADS)

Zhou, Tian; Han, Biao; Han, Lin; Li, Christopher; Department of Materials Science; Engineering Team; School of Biomedical Engineering, Science; Health Systems Team

2015-03-01

Molecular Velcro is commonly seen in biological systems as the formation of strong physical entanglement at molecular scale could induce strong adhesion, which is crucial to many biological processes. To mimic this structure, we designed, and fabricated polymer loop brushes using polymer single crystals with desired surface functionality and controlled chain folding. Compared with reported loop brushes fabricated using triblock copolymers, the present loop bushes have precise loop sizes, loop grafting density, and well controlled tethering locations on the solid surface. Atomic force microscopy-based force spectroscopy measurements using a polymer chain coated probe reveal that the adhesion force are significantly enhanced on the loop brush surface as compared with its single-strand counterpart. This study directly shows the effect of polymer brush conformation on their properties, and suggests a promising strategy for advanced polymer surface design.
Charge transport in organic semiconductors.

PubMed

Bässler, Heinz; Köhler, Anna

2012-01-01

Modern optoelectronic devices, such as light-emitting diodes, field-effect transistors and organic solar cells require well controlled motion of charges for their efficient operation. The understanding of the processes that determine charge transport is therefore of paramount importance for designing materials with improved structure-property relationships. Before discussing different regimes of charge transport in organic semiconductors, we present a brief introduction into the conceptual framework in which we interpret the relevant photophysical processes. That is, we compare a molecular picture of electronic excitations against the Su-Schrieffer-Heeger semiconductor band model. After a brief description of experimental techniques needed to measure charge mobilities, we then elaborate on the parameters controlling charge transport in technologically relevant materials. Thus, we consider the influences of electronic coupling between molecular units, disorder, polaronic effects and space charge. A particular focus is given to the recent progress made in understanding charge transport on short time scales and short length scales. The mechanism for charge injection is briefly addressed towards the end of this chapter.
Molecular quenching and relaxation in a plasmonic tunable system

NASA Astrophysics Data System (ADS)

Baffou, Guillaume; Girard, Christian; Dujardin, Erik; Colas Des Francs, Gérard; Martin, Olivier J. F.

2008-03-01

Molecular fluorescence decay is significantly modified when the emitting molecule is located near a plasmonic structure. When the lateral sizes of such structures are reduced to nanometer-scale cross sections, they can be used to accurately control and amplify the emission rate. In this Rapid Communication, we extend Green’s dyadic method to quantitatively investigate both radiative and nonradiative decay channels experienced by a single fluorescent molecule confined in an adjustable dielectric-metal nanogap. The technique produces data in excellent agreement with current experimental work.
Acetylcholine molecular arrays enable quantum information processing

NASA Astrophysics Data System (ADS)

Tamulis, Arvydas; Majauskaite, Kristina; Talaikis, Martynas; Zborowski, Krzysztof; Kairys, Visvaldas

2017-09-01

We have found self-assembly of four neurotransmitter acetylcholine (ACh) molecular complexes in a water molecules environment by using geometry optimization with DFT B97d method. These complexes organizes to regular arrays of ACh molecules possessing electronic spins, i.e. quantum information bits. These spin arrays could potentially be controlled by the application of a non-uniform external magnetic field. The proper sequence of resonant electromagnetic pulses would then drive all the spin groups into the 3-spin entangled state and proceed large scale quantum information bits.
Hierarchically Patterned Noncovalent Functionalization of 2D Materials by Controlled Langmuir-Schaefer Conversion.

PubMed

Davis, Tyson C; Bang, Jae Jin; Brooks, Jacob T; McMillan, David G; Claridge, Shelley A

2018-01-30

Noncovalent monolayer chemistries are often used to functionalize 2D materials. Nanoscopic ligand ordering has been widely demonstrated (e.g., lying-down lamellar phases of functional alkanes); however, combining this control with micro- and macroscopic patterning for practical applications remains a significant challenge. A few reports have demonstrated that standing phase Langmuir films on water can be converted into nanoscopic lying-down molecular domains on 2D substrates (e.g., graphite), using horizontal dipping (Langmuir-Schaefer, LS, transfer). Molecular patterns are known to form at scales up to millimeters in Langmuir films, suggesting the possibility of transforming such structures into functional patterns on 2D materials. However, to our knowledge, this approach has not been investigated, and the rules governing LS conversion are not well understood. In part, this is because the conversion process is mechanistically very different from classic LS transfer of standing phases; challenges also arise due to the need to characterize structure in noncovalently adsorbed ligand layers <0.5 nm thick, at scales ranging from millimeters to nanometers. Here, we show that scanning electron microscopy enables diynoic acid lying-down phases to be imaged across this range of scales; using this structural information, we establish conditions for LS conversion to create hierarchical microscopic and nanoscopic functional patterns. Such control opens the door to tailoring noncovalent surface chemistry of 2D materials to pattern local interactions with the environment.
Molecular control of normal and acrocona mutant seed cone development in Norway spruce (Picea abies) and the evolution of conifer ovule-bearing organs.

PubMed

Carlsbecker, Annelie; Sundström, Jens F; Englund, Marie; Uddenberg, Daniel; Izquierdo, Liz; Kvarnheden, Anders; Vergara-Silva, Francisco; Engström, Peter

2013-10-01

Reproductive organs in seed plants are morphologically divergent and their evolutionary history is often unclear. The mechanisms controlling their development have been extensively studied in angiosperms but are poorly understood in conifers and other gymnosperms. Here, we address the molecular control of seed cone development in Norway spruce, Picea abies. We present expression analyses of five novel MADS-box genes in comparison with previously identified MADS and LEAFY genes at distinct developmental stages. In addition, we have characterized the homeotic transformation from vegetative shoot to female cone and associated changes in regulatory gene expression patterns occurring in the acrocona mutant. The analyses identified genes active at the onset of ovuliferous and ovule development and identified expression patterns marking distinct domains of the ovuliferous scale. The reproductive transformation in acrocona involves the activation of all tested genes normally active in early cone development, except for an AGAMOUS-LIKE6/SEPALLATA (AGL6/SEP) homologue. This absence may be functionally associated with the nondeterminate development of the acrocona ovule-bearing scales. Our morphological and gene expression analyses give support to the hypothesis that the modern cone is a complex structure, and the ovuliferous scale the result of reductions and compactions of an ovule-bearing axillary short shoot in cones of Paleozoic conifers. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.
Controlling destructive quantum interference in tunneling junctions comprising self-assembled monolayers via bond topology and functional groups† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc00165k

PubMed Central

Zhang, Yanxi; Ye, Gang; Soni, Saurabh; Qiu, Xinkai; Krijger, Theodorus L.; Jonkman, Harry T.; Carlotti, Marco; Sauter, Eric; Zharnikov, Michael

2018-01-01

Quantum interference effects (QI) are of interest in nano-scale devices based on molecular tunneling junctions because they can affect conductance exponentially through minor structural changes. However, their utilization requires the prediction and deterministic control over the position and magnitude of QI features, which remains a significant challenge. In this context, we designed and synthesized three benzodithiophenes based molecular wires; one linearly-conjugated, one cross-conjugated and one cross-conjugated quinone. Using eutectic Ga–In (EGaIn) and CP-AFM, we compared them to a well-known anthraquinone in molecular junctions comprising self-assembled monolayers (SAMs). By combining density functional theory and transition voltage spectroscopy, we show that the presence of an interference feature and its position can be controlled independently by manipulating bond topology and electronegativity. This is the first study to separate these two parameters experimentally, demonstrating that the conductance of a tunneling junction depends on the position and depth of a QI feature, both of which can be controlled synthetically. PMID:29896382
Molecular transport through capillaries made with atomic-scale precision

NASA Astrophysics Data System (ADS)

Radha, B.; Esfandiar, A.; Wang, F. C.; Rooney, A. P.; Gopinadhan, K.; Keerthi, A.; Mishchenko, A.; Janardanan, A.; Blake, P.; Fumagalli, L.; Lozada-Hidalgo, M.; Garaj, S.; Haigh, S. J.; Grigorieva, I. V.; Wu, H. A.; Geim, A. K.

2016-10-01

Nanometre-scale pores and capillaries have long been studied because of their importance in many natural phenomena and their use in numerous applications. A more recent development is the ability to fabricate artificial capillaries with nanometre dimensions, which has enabled new research on molecular transport and led to the emergence of nanofluidics. But surface roughness in particular makes it challenging to produce capillaries with precisely controlled dimensions at this spatial scale. Here we report the fabrication of narrow and smooth capillaries through van der Waals assembly, with atomically flat sheets at the top and bottom separated by spacers made of two-dimensional crystals with a precisely controlled number of layers. We use graphene and its multilayers as archetypal two-dimensional materials to demonstrate this technology, which produces structures that can be viewed as if individual atomic planes had been removed from a bulk crystal to leave behind flat voids of a height chosen with atomic-scale precision. Water transport through the channels, ranging in height from one to several dozen atomic planes, is characterized by unexpectedly fast flow (up to 1 metre per second) that we attribute to high capillary pressures (about 1,000 bar) and large slip lengths. For channels that accommodate only a few layers of water, the flow exhibits a marked enhancement that we associate with an increased structural order in nanoconfined water. Our work opens up an avenue to making capillaries and cavities with sizes tunable to ångström precision, and with permeation properties further controlled through a wide choice of atomically flat materials available for channel walls.
Graph-based linear scaling electronic structure theory.

PubMed

Niklasson, Anders M N; Mniszewski, Susan M; Negre, Christian F A; Cawkwell, Marc J; Swart, Pieter J; Mohd-Yusof, Jamal; Germann, Timothy C; Wall, Michael E; Bock, Nicolas; Rubensson, Emanuel H; Djidjev, Hristo

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.
Graph-based linear scaling electronic structure theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niklasson, Anders M. N., E-mail: amn@lanl.gov; Negre, Christian F. A.; Cawkwell, Marc J.

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.
3D-Printable Photochromic Molecular Materials for Reversible Information Storage.

PubMed

Wales, Dominic J; Cao, Qun; Kastner, Katharina; Karjalainen, Erno; Newton, Graham N; Sans, Victor

2018-06-01

The formulation of advanced molecular materials with bespoke polymeric ionic-liquid matrices that stabilize and solubilize hybrid organic-inorganic polyoxometalates and allow their processing by additive manufacturing, is effectively demonstrated. The unique photo and redox properties of nanostructured polyoxometalates are translated across the scales (from molecular design to functional materials) to yield macroscopic functional devices with reversible photochromism. These properties open a range of potential applications including reversible information storage based on controlled topological and temporal reduction/oxidation of pre-formed printed devices. This approach pushes the boundaries of 3D printing to the molecular limits, allowing the freedom of design enabled by 3D printing to be coupled with the molecular tuneability of polymerizable ionic liquids and the photoactivity and orbital engineering possible with hybrid polyoxometalates. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Coherent molecular transistor: control through variation of the gate wave function.

PubMed

Ernzerhof, Matthias

2014-03-21

In quantum interference transistors (QUITs), the current through the device is controlled by variation of the gate component of the wave function that interferes with the wave function component joining the source and the sink. Initially, mesoscopic QUITs have been studied and more recently, QUITs at the molecular scale have been proposed and implemented. Typically, in these devices the gate lead is subjected to externally adjustable physical parameters that permit interference control through modifications of the gate wave function. Here, we present an alternative model of a molecular QUIT in which the gate wave function is directly considered as a variable and the transistor operation is discussed in terms of this variable. This implies that we specify the gate current as well as the phase of the gate wave function component and calculate the resulting current through the source-sink channel. Thus, we extend on prior works that focus on the phase of the gate wave function component as a control parameter while having zero or certain discrete values of the current. We address a large class of systems, including finite graphene flakes, and obtain analytic solutions for how the gate wave function controls the transistor.
A robust molecular probe for Ångstrom-scale analytics in liquids

PubMed Central

Nirmalraj, Peter; Thompson, Damien; Dimitrakopoulos, Christos; Gotsmann, Bernd; Dumcenco, Dumitru; Kis, Andras; Riel, Heike

2016-01-01

Traditionally, nanomaterial profiling using a single-molecule-terminated scanning probe is performed at the vacuum–solid interface often at a few Kelvin, but is not a notion immediately associated with liquid–solid interface at room temperature. Here, using a scanning tunnelling probe functionalized with a single C60 molecule stabilized in a high-density liquid, we resolve low-dimensional surface defects, atomic interfaces and capture Ångstrom-level bond-length variations in single-layer graphene and MoS2. Atom-by-atom controllable imaging contrast is demonstrated at room temperature and the electronic structure of the C60–metal probe complex within the encompassing liquid molecules is clarified using density functional theory. Our findings demonstrates that operating a robust single-molecular probe is not restricted to ultra-high vacuum and cryogenic settings. Hence the scope of high-precision analytics can be extended towards resolving sub-molecular features of organic elements and gauging ambient compatibility of emerging layered materials with atomic-scale sensitivity under experimentally less stringent conditions. PMID:27516157
Terasonic Excitations in 2D Gold Nanoparticle Arrays in a Water Matrix as Revealed by Atomistic Simulations

DOE PAGES

Bolmatov, Dima; Zhernenkov, Mikhail; Zav’yalov, Dmitry; ...

2016-08-19

Here in this work we report on terahertz phononic excitations in 2D gold nanoparticle arrays in a water matrix through a series of large-scale molecular dynamics simulations. For the first time, we observe acoustic Dirac-like crossings in H (H 2O) atomic (molecular) networks which emerge due to an intraband phononic scattering. These crossings are the phononic fingerprints of ice-like arrangements of H (H 2O) atomic (molecular) networks at nanometer scale. We reveal how phononic excitations in metallic nanoparticles and the water matrix reciprocally impact on one another providing the mechanism for the THz phononics manipulation via structural engineering. In addition,more » we show that by tuning the arrangement of 2D gold nanoparticle assemblies the Au phononic polarizations experience sub-terahertz hybridization (Kohn anomaly) due to surface electron-phonon relaxation processes. This opens the way for the sound control and manipulation in soft matter metamaterials at nanoscale.« less
Effect of critical molecular weight of PEO in epoxy/EPO blends as characterized by advanced DSC and solid-state NMR

NASA Astrophysics Data System (ADS)

Wang, Xiaoliang; Lu, Shoudong; Sun, Pingchuan; Xue, Gi

2013-03-01

The differential scanning calorimetry (DSC) and solid state NMR have been used to systematically study the length scale of the miscibility and local dynamics of the epoxy resin/poly(ethylene oxide) (ER/PEO) blends with different PEO molecular weight. By DSC, we found that the diffusion behavior of PEO with different Mw is an important factor in controlling these behaviors upon curing. We further employed two-dimensional 13C-{1H}PISEMA NMR experiment to elucidate the possible weak interaction and detailed local dynamics in ER/PEO blends. The CH2O group of PEO forms hydrogen bond with hydroxyl proton of cured-ER ether group, and its local dynamics frozen by such interaction. Our finding indicates that molecular weight (Mw) of PEO is a crucial factor in controlling the miscibility, chain dynamics and hydrogen bonding interaction in these blends.
Nanotechnology: Fundamental Principles and Applications

NASA Astrophysics Data System (ADS)

Ranjit, Koodali T.; Klabunde, Kenneth J.

Nanotechnology research is based primarily on molecular manufacturing. Although several definitions have been widely used in the past to describe the field of nanotechnology, it is worthwhile to point out that the National Nanotechnology Initiative (NNI), a federal research and development scheme approved by the congress in 2001 defines nanotechnology only if the following three aspects are involved: (1) research and technology development at the atomic, molecular, or macromolecular levels, in the length scale of approximately 1-100 nanometer range, (2) creating and using structures, devices, and systems that have novel properties and functions because of their small and/or intermediate size, and (3) ability to control or manipulate on the atomic scale. Nanotechnology in essence is the technology based on the manipulation of individual atoms and molecules to build complex structures that have atomic specifications.
Diffusive, Displacive Deformations and Local Phase Transformation Govern the Mechanics of Layered Crystals: The Case Study of Tobermorite.

PubMed

Tao, Lei; Shahsavari, Rouzbeh

2017-07-19

Understanding the deformation mechanisms underlying the mechanical behavior of materials is the key to fundamental and engineering advances in materials' performance. Herein, we focus on crystalline calcium-silicate-hydrates (C-S-H) as a model system with applications in cementitious materials, bone-tissue engineering, drug delivery and refractory materials, and use molecular dynamics simulation to investigate its loading geometry dependent mechanical properties. By comparing various conventional (e.g. shear, compression and tension) and nano-indentation loading geometries, our findings demonstrate that the former loading leads to size-independent mechanical properties while the latter results in size-dependent mechanical properties at the nanometer scales. We found three key mechanisms govern the deformation and thus mechanics of the layered C-S-H: diffusive-controlled and displacive-controlled deformation mechanisms, and strain gradient with local phase transformations. Together, these elaborately classified mechanisms provide deep fundamental understanding and new insights on the relationship between the macro-scale mechanical properties and underlying molecular deformations, providing new opportunities to control and tune the mechanics of layered crystals and other complex materials such as glassy C-S-H, natural composite structures, and manmade laminated structures.
Universal scaling for polymer chain scission in turbulence

PubMed Central

Vanapalli, Siva A.; Ceccio, Steven L.; Solomon, Michael J.

2006-01-01

We report that previous polymer chain scission experiments in strong flows, long analyzed according to accepted laminar flow scission theories, were in fact affected by turbulence. We reconcile existing anomalies between theory and experiment with the hypothesis that the local stress at the Kolmogorov scale generates the molecular tension leading to polymer covalent bond breakage. The hypothesis yields a universal scaling for polymer scission in turbulent flows. This surprising reassessment of over 40 years of experimental data simplifies the theoretical picture of polymer dynamics leading to scission and allows control of scission in commercial polymers and genomic DNA. PMID:17075043
Isolated molecular dopants in pentacene observed by scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Ha, Sieu D.; Kahn, Antoine

2009-11-01

Doping is essential to the control of electronic structure and conductivity of semiconductor materials. Whereas doping of inorganic semiconductors is well established, doping of organic molecular semiconductors is still relatively poorly understood. Using scanning tunneling microscopy, we investigate, at the molecular scale, surface and subsurface tetrafluoro-tetracyanoquinodimethane p -dopants in the prototypical molecular semiconductor pentacene. Surface dopants diffuse to pentacene vacancies and appear as negatively charged centers, consistent with the standard picture of an ionized acceptor. Subsurface dopants, however, have the effect of a positive charge, evidence that the donated hole is localized by the parent acceptor counterion, in contrast to the model of doping in inorganic semiconductors. Scanning tunneling spectroscopy shows that the electron potential energy is locally lowered near a subsurface dopant feature, in agreement with the localized hole model.
Ranges of Applicability for the Continuum-beam Model in the Constitutive Analysis of Carbon Nanotubes: Nanotubes or Nano-beams?

NASA Technical Reports Server (NTRS)

Harik, Vasyl Michael; Bushnell, Dennis M. (Technical Monitor)

2001-01-01

Ranges of validity for the continuum-beam model, the length-scale effects and continuum assumptions are analyzed in the framework of scaling analysis of NT structure. Two coupled criteria for the applicability of the continuum model are presented. Scaling analysis of NT buckling and geometric parameters (e.g., diameter and length) is carried out to determine the key non-dimensional parameters that control the buckling strains and modes of NT buckling. A model applicability map, which represents two classes of NTs, is constructed in the space of non-dimensional parameters. In an analogy with continuum mechanics, a mechanical law of geometric similitude is presented for two classes of beam-like NTs having different geometries. Expressions for the critical buckling loads and strains are tailored for the distinct groups of NTs and compared with the data provided by the molecular dynamics simulations. Implications for molecular dynamics simulations and the NT-based scanning probes are discussed.

Modeling of molecular diffusion and thermal conduction with multi-particle interaction in compressible turbulence

NASA Astrophysics Data System (ADS)

Tai, Y.; Watanabe, T.; Nagata, K.

2018-03-01

A mixing volume model (MVM) originally proposed for molecular diffusion in incompressible flows is extended as a model for molecular diffusion and thermal conduction in compressible turbulence. The model, established for implementation in Lagrangian simulations, is based on the interactions among spatially distributed notional particles within a finite volume. The MVM is tested with the direct numerical simulation of compressible planar jets with the jet Mach number ranging from 0.6 to 2.6. The MVM well predicts molecular diffusion and thermal conduction for a wide range of the size of mixing volume and the number of mixing particles. In the transitional region of the jet, where the scalar field exhibits a sharp jump at the edge of the shear layer, a smaller mixing volume is required for an accurate prediction of mean effects of molecular diffusion. The mixing time scale in the model is defined as the time scale of diffusive effects at a length scale of the mixing volume. The mixing time scale is well correlated for passive scalar and temperature. Probability density functions of the mixing time scale are similar for molecular diffusion and thermal conduction when the mixing volume is larger than a dissipative scale because the mixing time scale at small scales is easily affected by different distributions of intermittent small-scale structures between passive scalar and temperature. The MVM with an assumption of equal mixing time scales for molecular diffusion and thermal conduction is useful in the modeling of the thermal conduction when the modeling of the dissipation rate of temperature fluctuations is difficult.
Preparation, characterization, and scale-up of ketoconazole with enhanced dissolution and bioavailability.

PubMed

Elder, Edmund J; Evans, Jonathan C; Scherzer, Brian D; Hitt, James E; Kupperblatt, Gary B; Saghir, Shakil A; Markham, Dan A

2007-07-01

Many new molecular entities targeted for pharmaceutical applications face serious development challenges because of poor water solubility. Although particle engineering technologies such as controlled precipitation have been shown to enhance aqueous dissolution and bioavailability of poorly water soluble active pharmaceutical ingredients, the data available are the results of laboratory-scale experiments. These technologies must be evaluated at larger scale to ensure that the property enhancement is scalable and that the modified drugs can be processed on conventional equipment. In experiments using ketoconazole as the model drug, the controlled precipitation process was shown to produce kg-scale modified drug powder with enhanced dissolution comparable to that of lab-scale powder. Ketoconazole was demonstrated to be stable throughout the controlled precipitation process, with a residual methanol level below the ICH limit. The modified crystalline powder can be formulated, and then compressed using conventional high-speed tableting equipment, and the resulting tablets showed bioavailability more than double that of commercial tablets. When appropriately protected from moisture, both the modified powder and tablets prepared from the modified powder showed no change in dissolution performance for at least 6 months following storage at accelerated conditions and for at least 18 months following storage at room temperature.
Superresolution Imaging using Single-Molecule Localization

PubMed Central

Patterson, George; Davidson, Michael; Manley, Suliana; Lippincott-Schwartz, Jennifer

2013-01-01

Superresolution imaging is a rapidly emerging new field of microscopy that dramatically improves the spatial resolution of light microscopy by over an order of magnitude (∼10–20-nm resolution), allowing biological processes to be described at the molecular scale. Here, we discuss a form of superresolution microscopy based on the controlled activation and sampling of sparse subsets of photoconvertible fluorescent molecules. In this single-molecule based imaging approach, a wide variety of probes have proved valuable, ranging from genetically encodable photoactivatable fluorescent proteins to photoswitchable cyanine dyes. These have been used in diverse applications of superresolution imaging: from three-dimensional, multicolor molecule localization to tracking of nanometric structures and molecules in living cells. Single-molecule-based superresolution imaging thus offers exciting possibilities for obtaining molecular-scale information on biological events occurring at variable timescales. PMID:20055680
Lightweight computational steering of very large scale molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beazley, D.M.; Lomdahl, P.S.

1996-09-01

We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show howmore » this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.« less
Nanomedicine – challenge and perspectives

PubMed Central

Riehemann, Kristina; Schneider, Stefan W.; Luger, Thomas A.; Godin, Biana; Ferrari, Mauro; Fuchs, Harald

2014-01-01

Nanomedicine introduces nanotechnology concepts into medicine and thus joins two large cross disciplinary fields with an unprecedented societal and economical potential arising from the natural combination of specific achievements in the respective fields. The common basis evolves from the molecular scale properties relevant in the two fields. Nanoanalytical tools such as local probes and molecular imaging techniques, allow us to characterize surface and interface properties at a nanometer scale at predefined locations, while elaborated chemical approaches offer the opportunity for the control and addressing of surfaces e. g. for targeted drug delivery, enhanced biocompatibility and neuroprosthetic purposes. This commonality opens a wide variety of economic fields both of industrial and clinical interests. However, concerns arise in this cross disciplinary area about toxicological aspects and ethical implications. This review gives an overview of selected recent developments of nanotechnology applied on medical objectives. PMID:19142939
A 17 GHz molecular rectifier

PubMed Central

Trasobares, J.; Vuillaume, D.; Théron, D.; Clément, N.

2016-01-01

Molecular electronics originally proposed that small molecules sandwiched between electrodes would accomplish electronic functions and enable ultimate scaling to be reached. However, so far, functional molecular devices have only been demonstrated at low frequency. Here, we demonstrate molecular diodes operating up to 17.8 GHz. Direct current and radio frequency (RF) properties were simultaneously measured on a large array of molecular junctions composed of gold nanocrystal electrodes, ferrocenyl undecanethiol molecules and the tip of an interferometric scanning microwave microscope. The present nanometre-scale molecular diodes offer a current density increase by several orders of magnitude compared with that of micrometre-scale molecular diodes, allowing RF operation. The measured S11 parameters show a diode rectification ratio of 12 dB which is linked to the rectification behaviour of the direct current conductance. From the RF measurements, we extrapolate a cut-off frequency of 520 GHz. A comparison with the silicon RF-Schottky diodes, architecture suggests that the RF-molecular diodes are extremely attractive for scaling and high-frequency operation. PMID:27694833
Charge migration and charge transfer in molecular systems

PubMed Central

Wörner, Hans Jakob; Arrell, Christopher A.; Banerji, Natalie; Cannizzo, Andrea; Chergui, Majed; Das, Akshaya K.; Hamm, Peter; Keller, Ursula; Kraus, Peter M.; Liberatore, Elisa; Lopez-Tarifa, Pablo; Lucchini, Matteo; Meuwly, Markus; Milne, Chris; Moser, Jacques-E.; Rothlisberger, Ursula; Smolentsev, Grigory; Teuscher, Joël; van Bokhoven, Jeroen A.; Wenger, Oliver

2017-01-01

The transfer of charge at the molecular level plays a fundamental role in many areas of chemistry, physics, biology and materials science. Today, more than 60 years after the seminal work of R. A. Marcus, charge transfer is still a very active field of research. An important recent impetus comes from the ability to resolve ever faster temporal events, down to the attosecond time scale. Such a high temporal resolution now offers the possibility to unravel the most elementary quantum dynamics of both electrons and nuclei that participate in the complex process of charge transfer. This review covers recent research that addresses the following questions. Can we reconstruct the migration of charge across a molecule on the atomic length and electronic time scales? Can we use strong laser fields to control charge migration? Can we temporally resolve and understand intramolecular charge transfer in dissociative ionization of small molecules, in transition-metal complexes and in conjugated polymers? Can we tailor molecular systems towards specific charge-transfer processes? What are the time scales of the elementary steps of charge transfer in liquids and nanoparticles? Important new insights into each of these topics, obtained from state-of-the-art ultrafast spectroscopy and/or theoretical methods, are summarized in this review. PMID:29333473
Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another?

PubMed

Mellis, Ian A; Raj, Arjun

2015-10-01

Small-scale molecular systems biology, by which we mean the understanding of a how a few parts work together to control a particular biological process, is predicated on the assumption that cellular regulation is arranged in a circuit-like structure. Results from the omics revolution have upset this vision to varying degrees by revealing a high degree of interconnectivity, making it difficult to develop a simple, circuit-like understanding of regulatory processes. We here outline the limitations of the small-scale systems biology approach with examples from research into genetic algorithms, genetics, transcriptional network analysis, and genomics. We also discuss the difficulties associated with deriving true understanding from the analysis of large data sets and propose that the development of new, intelligent, computational tools may point to a way forward. Throughout, we intentionally oversimplify and talk about things in which we have little expertise, and it is likely that many of our arguments are wrong on one level or another. We do believe, however, that developing a true understanding via molecular systems biology will require a fundamental rethinking of our approach, and our goal is to provoke thought along these lines. © 2015 Mellis and Raj; Published by Cold Spring Harbor Laboratory Press.
Effect of mineral surface properties (alumina, kaolinite) on the sorptive fractionation mechanisms of soil fulvic acids: Molecular-scale ESI-MS studies

NASA Astrophysics Data System (ADS)

Fleury, Guillaume; Del Nero, Mirella; Barillon, Rémi

2017-01-01

We addressed the effects of mineral surface properties (kaolinite versus Al-oxide) on the sorption-driven fractionation of a soil fulvic acid (FA) at acidic pH, mainly by means of ESI(-)-FTMS analysis of initial and supernatant solutions of FA sorption batch experiments. The MS data provided clear molecular-scale evidence of distinct mechanisms and molecular parameters controlling the FA fractionation upon its sorption on clay and oxide surfaces, respectively. Identification of sorbing and not-sorbing FA compounds in kaolinite-solution systems revealed a weak fractionation among members of sbnd CO2 series of aliphatics or not-condensed aromatics (NCAs) at pH 3.8, and almost no sorption of poorly-oxygenated polycyclic aromatic compounds (PACs) and NCAs. This first molecular-scale description of a FA fractionation in a clay-solution system suggests that H-bonding with low affinity sites (aluminol/silanol) on the basal planes of the clay particles is the main mechanism of sorption. Due to the predominance of such weak and poorly-selective mechanism, the sorption of aliphatic and NCA molecules bearing oxygenated functionalities was prevented at pH 5, due to dissolved Al competing successfully for their coordination. In contrast, a strong FA fractionation was observed onto alumina, with a preferential retention of PACs and highly-oxygenated aliphatics and NCAs. The major part of the poorly oxygenated aliphatics was left in solution. The sorption degree of NCAs and aliphatics was strongly correlated with molecular acidity. For PACs and poorly-oxygenated NCAs, the sorption was driven by reactions of surface ligand exchange (for the most oxygenated compounds) or by hydrophobic interactions (for the least oxygenated compounds).
Preface: Special Topic on Frontiers in Molecular Scale Electronics

NASA Astrophysics Data System (ADS)

Evers, Ferdinand; Venkataraman, Latha

2017-03-01

The electronic, mechanical, and thermoelectric properties of molecular scale devices have fascinated scientists across several disciplines in natural sciences and engineering. The interest is partially technological, driven by the fast miniaturization of integrated circuits that now have reached characteristic features at the nanometer scale. Equally important, a very strong incentive also exists to elucidate the fundamental aspects of structure-function relations for nanoscale devices, which utilize molecular building blocks as functional units. Thus motivated, a rich research field has established itself, broadly termed "Molecular Electronics," that hosts a plethora of activities devoted to this goal in chemistry, physics, and electrical engineering. This Special Topic on Frontiers of Molecular Scale Electronics captures recent theoretical and experimental advances in the field.
An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids.

PubMed

Dahlberg, Jerry; Tkacik, Peter T; Mullany, Brigid; Fleischhauer, Eric; Shahinian, Hossein; Azimi, Farzad; Navare, Jayesh; Owen, Spencer; Bisel, Tucker; Martin, Tony; Sholar, Jodie; Keanini, Russell G

2017-12-04

An analog, macroscopic method for studying molecular-scale hydrodynamic processes in dense gases and liquids is described. The technique applies a standard fluid dynamic diagnostic, particle image velocimetry (PIV), to measure: i) velocities of individual particles (grains), extant on short, grain-collision time-scales, ii) velocities of systems of particles, on both short collision-time- and long, continuum-flow-time-scales, iii) collective hydrodynamic modes known to exist in dense molecular fluids, and iv) short- and long-time-scale velocity autocorrelation functions, central to understanding particle-scale dynamics in strongly interacting, dense fluid systems. The basic system is composed of an imaging system, light source, vibrational sensors, vibrational system with a known media, and PIV and analysis software. Required experimental measurements and an outline of the theoretical tools needed when using the analog technique to study molecular-scale hydrodynamic processes are highlighted. The proposed technique provides a relatively straightforward alternative to photonic and neutron beam scattering methods traditionally used in molecular hydrodynamic studies.
Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Simulations of the Molecular Crystal alphaRDX

DTIC Science & Technology

2013-08-01

potential for HMX / RDX (3, 9). ...................................................................................8 1 1. Purpose This work...6 dispersion and electrostatic interactions. Constants for the SB potential are given in table 1. 8 Table 1. SB potential for HMX / RDX (3, 9...modeling dislocations in the energetic molecular crystal RDX using the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) molecular
Nanoscale Controls on CO2-water-rock Interactions in Saline Reservoirs

NASA Astrophysics Data System (ADS)

Deyoreo, J.; Depaolo, D. J.

2009-12-01

It is becoming increasingly widely recognized that geologic sequestration of CO2, when combined with economical means of capture, may be one of the most effective approaches to reducing net CO2 emissions to the atmosphere over the next century. Injection of CO2 into saline geologic formations involves forcing a buoyant, low-viscosity fluid into a more dense, higher viscosity fluid. The difference in wetting properties of the two fluids, their partial miscibility, the fact that CO2 and H2O form an acid, and the heterogeneity of geologic formations combine to make the flow and transport details fascinating but difficult to fully characterize and predict. A major question is whether the flow of CO2 into subsurface formations, the efficiency of pore space filling, and the trapping efficiency can be not only predicted but controlled over the decades of injection that might be associated with the life of a power plant. The major technological gaps to controlling and ultimately sequestering subsurface CO2 can be traced to far-from-equilibrum processes that originate at the molecular and nanoscale, but are expressed as complex emergent behavior at larger scales. Essential knowledge gaps involve the effects of nanoscale confinement on material properties, flow and chemical reactions, the effects of nanoparticles, mineral surface dynamics, and microbiota on mineral dissolution/precipitation and fluid flow, and the dynamics of fluid-fluid and fluid-mineral interfaces. To address these scientific and technical challenges, the Energy Frontier Research Center recently established, involving collaboration between LBNL, ORNL, MIT, UC Berkeley, UC Davis and LLNL, will attempt to bring new approaches to the study of nanoscale phenomena in fluid-rock systems to bear on the problem of CO2 behavior in saline formations. The stated goal is to use molecular, nanoscale, and pore-network scale approaches to control flow, dissolution, and precipitation in deep subsurface rock formations to achieve the efficient filling of pore space while maximizing solubility and mineral trapping and reducing potential leakage. Advanced knowledge of these small-scale processes is an important step toward developing a next-generation predictive capability for reactive transport of CO2-brine systems. The Center involves scientists with expertise in hydrology, geochemistry, materials science, mineralogy, chemistry, microbiology, geophysics, and reactive transport modeling and simulation. This presentation will describe the initial stages of some of the research, which in total involves the use of synchrotron light sources, neutron scattering methods, NanoSIMS, molecular dynamics simulations, thermochemistry, molecular biology, nanotechnology, laboratory scale experiments, and advanced computation applied to flow and reactive transport in heterogeneous porous media. The Center for Nanoscale Control of Geologic CO2 key personnel: Director - D. DePaolo, Co-Director - J. DeYoreo; Research Area Leads - K. Knauss (LBNL), G. Waychunas (LBNL), J. Banfield (UCB/LBNL), A Navrotsky (UC Davis), F.J. Ryerson (LLNL); G. Sposito (UCB/LBNL), T. Tokunaga (LBNL), D. Cole (ORNL), C. Steefel (LBNL), D. Rothman (MIT), S. Pride (LBNL).
Preface: Special Topic on Atomic and Molecular Layer Processing: Deposition, Patterning, and Etching

NASA Astrophysics Data System (ADS)

Engstrom, James R.; Kummel, Andrew C.

2017-02-01

Thin film processing technologies that promise atomic and molecular scale control have received increasing interest in the past several years, as traditional methods for fabrication begin to reach their fundamental limits. Many of these technologies involve at their heart phenomena occurring at or near surfaces, including adsorption, gas-surface reactions, diffusion, desorption, and re-organization of near-surface layers. Moreover many of these phenomena involve not just reactions occurring under conditions of local thermodynamic equilibrium but also the action of energetic species including electrons, ions, and hyperthermal neutrals. There is a rich landscape of atomic and molecular scale interactions occurring in these systems that is still not well understood. In this Special Topic Issue of The Journal of Chemical Physics, we have collected recent representative examples of work that is directed at unraveling the mechanistic details concerning atomic and molecular layer processing, which will provide an important framework from which these fields can continue to develop. These studies range from the application of theory and computation to these systems to the use of powerful experimental probes, such as X-ray synchrotron radiation, probe microscopies, and photoelectron and infrared spectroscopies. The work presented here helps in identifying some of the major challenges and direct future activities in this exciting area of research involving atomic and molecular layer manipulation and fabrication.
Preface: Special Topic on Atomic and Molecular Layer Processing: Deposition, Patterning, and Etching.

PubMed

Engstrom, James R; Kummel, Andrew C

2017-02-07

Thin film processing technologies that promise atomic and molecular scale control have received increasing interest in the past several years, as traditional methods for fabrication begin to reach their fundamental limits. Many of these technologies involve at their heart phenomena occurring at or near surfaces, including adsorption, gas-surface reactions, diffusion, desorption, and re-organization of near-surface layers. Moreover many of these phenomena involve not just reactions occurring under conditions of local thermodynamic equilibrium but also the action of energetic species including electrons, ions, and hyperthermal neutrals. There is a rich landscape of atomic and molecular scale interactions occurring in these systems that is still not well understood. In this Special Topic Issue of The Journal of Chemical Physics, we have collected recent representative examples of work that is directed at unraveling the mechanistic details concerning atomic and molecular layer processing, which will provide an important framework from which these fields can continue to develop. These studies range from the application of theory and computation to these systems to the use of powerful experimental probes, such as X-ray synchrotron radiation, probe microscopies, and photoelectron and infrared spectroscopies. The work presented here helps in identifying some of the major challenges and direct future activities in this exciting area of research involving atomic and molecular layer manipulation and fabrication.
Changes in Chromatin Compaction During the Cell Cycle Revealed by Micrometer-Scale Measurement of Molecular Flow in the Nucleus

PubMed Central

Hinde, Elizabeth; Cardarelli, Francesco; Digman, Michelle A.; Gratton, Enrico

2012-01-01

We present a quantitative fluctuation-based assay to measure the degree of local chromatin compaction and investigate how chromatin density regulates the diffusive path adopted by an inert protein in dividing cells. The assay uses CHO-K1 cells coexpressing untagged enhanced green fluorescent protein (EGFP) and histone H2B tagged mCherry. We measure at the single-cell level the EGFP localization and molecular flow patterns characteristic of each stage of chromatin compaction from mitosis through interphase by means of pair-correlation analysis. We find that the naturally occurring changes in chromatin organization impart a regulation on the spatial distribution and temporal dynamics of EGFP within the nucleus. Combined with the analysis of Ca2+ intracellular homeostasis during cell division, EGFP flow regulation can be interpreted as the result of controlled changes in chromatin compaction. For the first time, to our knowledge, we were able to probe chromatin compaction on the micrometer scale, where the regulation of molecular diffusion may become relevant for many cellular processes. PMID:22325293
Synchrotron-based X-ray Fluorescence Microscopy in Conjunction with Nanoindentation to Study Molecular-Scale Interactions of Phenol-Formaldehyde in Wood Cell Walls

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jakes, Joseph E.; Hunt, Chris G.; Yelle, Daniel J.

Understanding and controlling molecular-scale interactions between adhesives and wood polymers are critical to accelerate the development of improved adhesives for advanced wood-based materials. The submicrometer resolution of synchrotron-based X-ray fluorescence microscopy (XFM) was found capable of mapping and quantifying infiltration of Br-labeled phenolformaldehyde (BrPF) into wood cell walls. Cell wall infiltration of five BrPF adhesives with different average molecular weights (MWs) was mapped. Nanoindentation on the same cell walls was performed to assess the effects of BrPF infiltration on cell wall hygromechanical properties. For the same amount of weight uptake, lower MW BrPF adhesives were found to be more effectivemore » at decreasing moisture-induced mechanical softening. This greater effectiveness of lower MW phenolic adhesives likely resulted from their ability to more intimately associate with water sorption sites in the wood polymers. Evidence also suggests that a BrPF interpenetrating polymer network (IPN) formed within the wood polymers, which might also decrease moisture sorption by mechanically restraining wood polymers during swelling.« less
High pressure study of molecular dynamics of protic ionic liquid lidocaine hydrochloride.

PubMed

Swiety-Pospiech, A; Wojnarowska, Z; Pionteck, J; Pawlus, S; Grzybowski, A; Hensel-Bielowka, S; Grzybowska, K; Szulc, A; Paluch, M

2012-06-14

In this paper, we investigate the effect of pressure on the molecular dynamics of protic ionic liquid lidocaine hydrochloride, a commonly used pharmaceutical, by means of dielectric spectroscopy and pressure-temperature-volume methods. We observed that near T(g) the pressure dependence of conductivity relaxation times reveals a peculiar behavior, which can be treated as a manifestation of decoupling between ion migration and structural relaxation times. Moreover, we discuss the validity of thermodynamic scaling in lidocaine HCl. We also employed the temperature-volume Avramov model to determine the value of pressure coefficient of glass transition temperature, dT(g)/dP|(P = 0.1). Finally, we investigate the role of thermal and density fluctuations in controlling of molecular dynamics of the examined compound.
Hey hey hey hey, it was the DNA

NASA Astrophysics Data System (ADS)

Williams, Martin A. K.

2016-05-01

The investigation of the emergence of spatial patterning in the density profiles of the individual elements of multicomponent systems was perhaps first popularised in a biophysical context by Turing’s work on embryogenesis in 1952. How molecular-scale properties transpire to produce patterns at larger scales continues to fascinate today. Now a model DNA-nanotube system, whose assemblies have been reported recently by Glaser et al (2016 New J. Phys. 18 055001), promises to reveal insights by allowing the mechanical properties of the underlying macromolecular entities to be controlled independently of their chemical nature.
Uncovering molecular processes in crystal nucleation and growth by using molecular simulation.

PubMed

Anwar, Jamshed; Zahn, Dirk

2011-02-25

Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

RNA Study Using DNA Nanotechnology.

PubMed

Tadakuma, Hisashi; Masubuchi, Takeya; Ueda, Takuya

2016-01-01

Transcription is one of the fundamental steps of gene expression, where RNA polymerases (RNAPs) bind to their template genes and make RNAs. In addition to RNAP and the template gene, many molecules such as transcription factors are involved. The interaction and the effect of these factors depend on the geometry. Molecular layout of these factors, RNAP and gene is thus important. DNA nanotechnology is a promising technology that allows controlling of the molecular layout in the range of nanometer to micrometer scale with nanometer resolution; thus, it is expected to expand the RNA study beyond the current limit. Copyright © 2016 Elsevier Inc. All rights reserved.
From nano- to macro-scale: nanotechnology approaches for spatially controlled delivery of bioactive factors for bone and cartilage engineering.

PubMed

Santo, Vítor E; Gomes, Manuela E; Mano, João F; Reis, Rui L

2012-07-01

The field of biomaterials has advanced towards the molecular and nanoscale design of bioactive systems for tissue engineering, regenerative medicine and drug delivery. Spatial cues are displayed in the 3D extracellular matrix and can include signaling gradients, such as those observed during chemotaxis. Architectures range from the nanometer to the centimeter length scales as exemplified by extracellular matrix fibers, cells and macroscopic shapes. The main focus of this review is the application of a biomimetic approach by the combination of architectural cues, obtained through the application of micro- and nanofabrication techniques, with the ability to sequester and release growth factors and other bioactive agents in a spatiotemporal controlled manner for bone and cartilage engineering.
Photoactuators for Direct Optical-to-Mechanical Energy Conversion: From Nanocomponent Assembly to Macroscopic Deformation.

PubMed

Hu, Ying; Li, Zhe; Lan, Tian; Chen, Wei

2016-12-01

Photoactuators with integrated optical-to-mechanical energy conversion capacity have attracted growing research interest in the last few decades due to their unique features of remote control and their wide applications ranging from bionic robots, biomedical devices, and switches to motors. For the photoactuator design, the energy conversion route and structure assembly are two important parts, which directly affect the performance of the photoactuators. In particular, the architectural designs at the molecular, nano-, micro-, and macro- level, are found to play a significant role in accumulating molecular-scale strain/stress to macroscale strain/stress. Here, recent progress on photoactuators based on photochemical and photothermal effects is summarized, followed by a discussion of the important assembly strategies for the amplification of the photoresponsive components at nanoscale to macroscopic scale motions. The application advancement of current photoactuators is also presented. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Nanomedicine: Tiny Particles and Machines Give Huge Gains

PubMed Central

Tong, Sheng; Fine, Eli J.; Lin, Yanni; Cradick, Thomas J.; Bao, Gang

2014-01-01

Nanomedicine is an emerging field that integrates nanotechnology, biomolecular engineering, life sciences and medicine; it is expected to produce major breakthroughs in medical diagnostics and therapeutics. Nano-scale structures and devices are compatible in size with proteins and nucleic acids in living cells. Therefore, the design, characterization and application of nano-scale probes, carriers and machines may provide unprecedented opportunities for achieving a better control of biological processes, and drastic improvements in disease detection, therapy, and prevention. Recent advances in nanomedicine include the development of nanoparticle-based probes for molecular imaging, nano-carriers for drug/gene delivery, multi-functional nanoparticles for theranostics, and molecular machines for biological and medical studies. This article provides an overview of the nanomedicine field, with an emphasis on nanoparticles for imaging and therapy, as well as engineered nucleases for genome editing. The challenges in translating nanomedicine approaches to clinical applications are discussed. PMID:24297494
Early and long-standing rheumatoid arthritis: distinct molecular signatures identified by gene-expression profiling in synovia

PubMed Central

Lequerré, Thierry; Bansard, Carine; Vittecoq, Olivier; Derambure, Céline; Hiron, Martine; Daveau, Maryvonne; Tron, François; Ayral, Xavier; Biga, Norman; Auquit-Auckbur, Isabelle; Chiocchia, Gilles; Le Loët, Xavier; Salier, Jean-Philippe

2009-01-01

Introduction Rheumatoid arthritis (RA) is a heterogeneous disease and its underlying molecular mechanisms are still poorly understood. Because previous microarray studies have only focused on long-standing (LS) RA compared to osteoarthritis, we aimed to compare the molecular profiles of early and LS RA versus control synovia. Methods Synovial biopsies were obtained by arthroscopy from 15 patients (4 early untreated RA, 4 treated LS RA and 7 controls, who had traumatic or mechanical lesions). Extracted mRNAs were used for large-scale gene-expression profiling. The different gene-expression combinations identified by comparison of profiles of early, LS RA and healthy synovia were linked to the biological processes involved in each situation. Results Three combinations of 719, 116 and 52 transcripts discriminated, respectively, early from LS RA, and early or LS RA from healthy synovia. We identified several gene clusters and distinct molecular signatures specifically expressed during early or LS RA, thereby suggesting the involvement of different pathophysiological mechanisms during the course of RA. Conclusions Early and LS RA have distinct molecular signatures with different biological processes participating at different times during the course of the disease. These results suggest that better knowledge of the main biological processes involved at a given RA stage might help to choose the most appropriate treatment. PMID:19563633
Control of femtosecond laser driven retro-Diels-Alder-like reaction of dicyclopentadiene

PubMed Central

Das, Dipak Kumar; Goswami, Tapas; Goswami, Debabrata

2013-01-01

Using femtosecond time resolved degenerate pump-probe mass spectrometry coupled with simple linearly chirped frequency modulated pulse, we elucidate that the dynamics of retro-Diels-Alder-like reaction of diclopentadiene (DCPD) to cyclopentadiene (CPD) in supersonic molecular beam occurs in ultrafast time scale. Negatively chirped pulse enhances the ion yield of CPD, as compared to positively chirped pulse. This indicates that by changing the frequency (chirp) of the laser pulse we can control the ion yield of a chemical reaction. PMID:23814449
Scaling behavior of immersed granular flows

NASA Astrophysics Data System (ADS)

Amarsid, L.; Delenne, J.-Y.; Mutabaruka, P.; Monerie, Y.; Perales, F.; Radjai, F.

2017-06-01

The shear behavior of granular materials immersed in a viscous fluid depends on fluid properties (viscosity, density), particle properties (size, density) and boundary conditions (shear rate, confining pressure). Using computational fluid dynamics simulations coupled with molecular dynamics for granular flow, and exploring a broad range of the values of parameters, we show that the parameter space can be reduced to a single parameter that controls the packing fraction and effective friction coefficient. This control parameter is a modified inertial number that incorporates viscous effects.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Sivak, David; Crooks, Gavin

A fundamental problem in modern thermodynamics is how a molecular-scale machine performs useful work, while operating away from thermal equilibrium without excessive dissipation. To this end, we derive a friction tensor that induces a Riemannian manifold on the space of thermodynamic states. Within the linear-response regime, this metric structure controls the dissipation of finite-time transformations, and bestows optimal protocols with many useful properties. We discuss the connection to the existing thermodynamic length formalism, and demonstrate the utility of this metric by solving for optimal control parameter protocols in a simple nonequilibrium model.
Protein based Block Copolymers

PubMed Central

Rabotyagova, Olena S.; Cebe, Peggy; Kaplan, David L.

2011-01-01

Advances in genetic engineering have led to the synthesis of protein-based block copolymers with control of chemistry and molecular weight, resulting in unique physical and biological properties. The benefits from incorporating peptide blocks into copolymer designs arise from the fundamental properties of proteins to adopt ordered conformations and to undergo self-assembly, providing control over structure formation at various length scales when compared to conventional block copolymers. This review covers the synthesis, structure, assembly, properties, and applications of protein-based block copolymers. PMID:21235251
Connecting the molecular scale to the continuum scale for diffusion processes in smectite-rich porous media.

PubMed

Bourg, Ian C; Sposito, Garrison

2010-03-15

In this paper, we address the manner in which the continuum-scale diffusive properties of smectite-rich porous media arise from their molecular- and pore-scale features. Our starting point is a successful model of the continuum-scale apparent diffusion coefficient for water tracers and cations, which decomposes it as a sum of pore-scale terms describing diffusion in macropore and interlayer "compartments." We then apply molecular dynamics (MD) simulations to determine molecular-scale diffusion coefficients D(interlayer) of water tracers and representative cations (Na(+), Cs(+), Sr(2+)) in Na-smectite interlayers. We find that a remarkably simple expression relates D(interlayer) to the pore-scale parameter δ(nanopore) ≤ 1, a constrictivity factor that accounts for the lower mobility in interlayers as compared to macropores: δ(nanopore) = D(interlayer)/D(0), where D(0) is the diffusion coefficient in bulk liquid water. Using this scaling expression, we can accurately predict the apparent diffusion coefficients of tracers H(2)0, Na(+), Sr(2+), and Cs(+) in compacted Na-smectite-rich materials.
Molecular biomimetics: utilizing nature's molecular ways in practical engineering.

PubMed

Tamerler, Candan; Sarikaya, Mehmet

2007-05-01

In nature, proteins are the machinery that accomplish many functions through their specific recognition and interactions in biological systems from single-celled to multicellular organisms. Biomolecule-material interaction is accomplished via molecular specificity, leading to the formation of controlled structures and functions at all scales of dimensional hierarchy. Through evolution, molecular recognition and, consequently, functions developed through successive cycles of mutation and selection. Using biology as a guide, we can now understand, engineer and control peptide-material interactions and exploit these to tailor novel materials and systems for practical applications. We adapted combinatorial biology protocols to display peptide libraries, either on the cell surface or on phages, to select short peptides specific to a variety of practical materials systems. Following the selection step, we determined the kinetics and stability of peptide binding experimentally to understand the bound peptide structure via modeling and its assembly via atomic force microscopy. The peptides were further engineered to have multiple repeats or their amino acid sequences varied to tailor their function. Both nanoparticles and flat inorganic substrates containing multimaterials patterned at the nano- and microscales were used for self-directed immobilization of molecular constructs. The molecular biomimetic approach opens up new avenues for the design and utilization of multifunctional molecular systems with wide ranging applications, from tissue engineering, drug delivery and biosensors, to nanotechnology and bioremediation. Here we give examples of protein-mediated functional materials in biology, peptide selection and engineering with affinity to inorganics, demonstrate potential utilizations in materials science, engineering and medicine, and describe future prospects.
Time-Resolved Small-Angle X-ray Scattering Reveals Millisecond Transitions of a DNA Origami Switch.

PubMed

Bruetzel, Linda K; Walker, Philipp U; Gerling, Thomas; Dietz, Hendrik; Lipfert, Jan

2018-04-11

Self-assembled DNA structures enable creation of specific shapes at the nanometer-micrometer scale with molecular resolution. The construction of functional DNA assemblies will likely require dynamic structures that can undergo controllable conformational changes. DNA devices based on shape complementary stacking interactions have been demonstrated to undergo reversible conformational changes triggered by changes in ionic environment or temperature. An experimentally unexplored aspect is how quickly conformational transitions of large synthetic DNA origami structures can actually occur. Here, we use time-resolved small-angle X-ray scattering to monitor large-scale conformational transitions of a two-state DNA origami switch in free solution. We show that the DNA device switches from its open to its closed conformation upon addition of MgCl 2 in milliseconds, which is close to the theoretical diffusive speed limit. In contrast, measurements of the dimerization of DNA origami bricks reveal much slower and concentration-dependent assembly kinetics. DNA brick dimerization occurs on a time scale of minutes to hours suggesting that the kinetics depend on local concentration and molecular alignment.
The shear flow processing of controlled DNA tethering and stretching for organic molecular electronics.

PubMed

Yu, Guihua; Kushwaha, Amit; Lee, Jungkyu K; Shaqfeh, Eric S G; Bao, Zhenan

2011-01-25

DNA has been recently explored as a powerful tool for developing molecular scaffolds for making reproducible and reliable metal contacts to single organic semiconducting molecules. A critical step in the process of exploiting DNA-organic molecule-DNA (DOD) array structures is the controlled tethering and stretching of DNA molecules. Here we report the development of reproducible surface chemistry for tethering DNA molecules at tunable density and demonstrate shear flow processing as a rationally controlled approach for stretching/aligning DNA molecules of various lengths. Through enzymatic cleavage of λ-phage DNA to yield a series of DNA chains of various lengths from 17.3 μm down to 4.2 μm, we have investigated the flow/extension behavior of these tethered DNA molecules under different flow strengths in the flow-gradient plane. We compared Brownian dynamic simulations for the flow dynamics of tethered λ-DNA in shear, and found our flow-gradient plane experimental results matched well with our bead-spring simulations. The shear flow processing demonstrated in our studies represents a controllable approach for tethering and stretching DNA molecules of various lengths. Together with further metallization of DNA chains within DOD structures, this bottom-up approach can potentially enable efficient and reliable fabrication of large-scale nanoelectronic devices based on single organic molecules, therefore opening opportunities in both fundamental understanding of charge transport at the single molecular level and many exciting applications for ever-shrinking molecular circuits.
Gesture Interaction Browser-Based 3D Molecular Viewer.

PubMed

Virag, Ioan; Stoicu-Tivadar, Lăcrămioara; Crişan-Vida, Mihaela

2016-01-01

The paper presents an open source system that allows the user to interact with a 3D molecular viewer using associated hand gestures for rotating, scaling and panning the rendered model. The novelty of this approach is that the entire application is browser-based and doesn't require installation of third party plug-ins or additional software components in order to visualize the supported chemical file formats. This kind of solution is suitable for instruction of users in less IT oriented environments, like medicine or chemistry. For rendering various molecular geometries our team used GLmol (a molecular viewer written in JavaScript). The interaction with the 3D models is made with Leap Motion controller that allows real-time tracking of the user's hand gestures. The first results confirmed that the resulting application leads to a better way of understanding various types of translational bioinformatics related problems in both biomedical research and education.
A well-scaling natural orbital theory

DOE PAGES

Gebauer, Ralph; Cohen, Morrel H.; Car, Roberto

2016-11-01

Here, we introduce an energy functional for ground-state electronic structure calculations. Its variables are the natural spin-orbitals of singlet many-body wave functions and their joint occupation probabilities deriving from controlled approximations to the two-particle density matrix that yield algebraic scaling in general, and Hartree–Fock scaling in its seniority-zero version. Results from the latter version for small molecular systems are compared with those of highly accurate quantum-chemical computations. The energies lie above full configuration interaction calculations, close to doubly occupied configuration interaction calculations. Their accuracy is considerably greater than that obtained from current density-functional theory approximations and from current functionals ofmore » the oneparticle density matrix.« less
A well-scaling natural orbital theory

PubMed Central

Gebauer, Ralph; Cohen, Morrel H.; Car, Roberto

2016-01-01

We introduce an energy functional for ground-state electronic structure calculations. Its variables are the natural spin-orbitals of singlet many-body wave functions and their joint occupation probabilities deriving from controlled approximations to the two-particle density matrix that yield algebraic scaling in general, and Hartree–Fock scaling in its seniority-zero version. Results from the latter version for small molecular systems are compared with those of highly accurate quantum-chemical computations. The energies lie above full configuration interaction calculations, close to doubly occupied configuration interaction calculations. Their accuracy is considerably greater than that obtained from current density-functional theory approximations and from current functionals of the one-particle density matrix. PMID:27803328
Templated electrokinetic directed chemical assembly for the fabrication of close-packed plasmonic metamolecules

NASA Astrophysics Data System (ADS)

Thrift, W. J.; Darvishzadeh-Varcheie, M.; Capolino, F.; Ragan, R.

2017-08-01

Colloidal self-assembly combined with templated surfaces holds the promise of fabricating large area devices in a low cost facile manner. This directed assembly approach improves the complexity of assemblies that can be achieved with self-assembly while maintaining advantages of molecular scale control. In this work, electrokinetic driving forces, i.e., electrohydrodynamic flow, are paired with chemical crosslinking between colloidal particles to form close-packed plasmonic metamolecules. This method addresses challenges of obtaining uniformity in nanostructure geometry and nanometer scale gap spacings in structures. Electrohydrodynamic flows yield robust driving forces between the template and nanoparticles as well as between nanoparticles on the surface promoting the assembly of close-packed metamolecules. Here, electron beam lithography defined Au pillars are used as seed structures that generate electrohydrodynamic flows. Chemical crosslinking between Au surfaces enables molecular control over gap spacings between nanoparticles and Au pillars. An as-fabricated structure is analyzed via full wave electromagnetic simulations and shown to produce large magnetic field enhancements on the order of 3.5 at optical frequencies. This novel method for directed self-assembly demonstrates the synergy between colloidal driving forces and chemical crosslinking for the fabrication of plasmonic metamolecules with unique electromagnetic properties.
Individual and molecular level effects of produced water contaminants on nauplii and adult females of Calanus finmarchicus.

PubMed

Jensen, Louise Kiel; Halvorsen, Elisabeth; Song, You; Hallanger, Ingeborg G; Hansen, Elisabeth Lindbo; Brooks, Steven J; Hansen, Bjørn Henrik; Tollefsen, Knut Erik

2016-01-01

In the Barents Sea region new petroleum fields are discovered yearly and extraction of petroleum products is expected to increase in the upcoming years. Despite enhanced technology and stricter governmental legislation, establishment of the petroleum industry in the Barents Sea may potentially introduce a new source of contamination to the area, as some discharges of produced water will be allowed. Whether the presence of produced water poses a risk to the Arctic marine life remains to be investigated. The aim of this study was to examine effects of exposure to several compounds found in produced water-a mixture of selected organic compounds (APW), radium-226 ((226)Ra), barium (Ba), and a scale inhibitor-on the copepod species Calanus finmarchicus. Experiments were performed using exposure concentrations at realistic levels based on those detected in the vicinity of known discharge points. The influence of lethal and sublethal effects on early life stages was determined and significantly lower survival in the APW exposure groups was found. In the Ba treatment the life stage development did not proceed to the same advanced stages as observed in the control (filtered sea water). The scale inhibitor and (226)Ra treatments showed no significant difference from control. In addition, adult females were exposed to APW, (226)Ra, and a mixture of the two. Both individual-level effects (egg production and feeding) and molecular-level effects (gene expression) were assessed. On the individual level endpoints, only treatments including APW produced an effect compared to control. However, on the molecular level the possibility that also (226)Ra induced toxicologically relevant effects cannot be ruled out.
Molecular Design of Squalene/Squalane Countertypes via the Controlled Oligomerization of Isoprene and Evaluation of Vaccine Adjuvant Applications.

PubMed

Adlington, Kevin; El Harfi, Jaouad; Li, Jianing; Carmichael, Kim; Guderian, Jeffrey A; Fox, Christopher B; Irvine, Derek J

2016-01-11

The potential to replace shark-derived squalene in vaccine adjuvant applications with synthetic squalene/poly(isoprene) oligomers, synthesized by the controlled oligomerization of isoprene is demonstrated. Following on from our previous work regarding the synthesis of poly(isoprene) oligomers, we demonstrate the ability to tune the molecular weight of the synthetic poly(isoprene) material beyond that of natural squalene, while retaining a final backbone structure that contained a minimum of 75% of 1,4 addition product and an acceptable polydispersity. The synthesis was successfully scaled from the 2 g to the 40 g scale both in the bulk (i.e., solvent free) and with the aid of additional solvent by utilizing catalytic chain transfer polymerization (CCTP) as the control method, such that the target molecular weight, acceptable dispersity levels, and the desired level of 1,4 addition in the backbone structure and an acceptable yield (∼60%) are achieved. Moreover, the stability and in vitro bioactivity of nanoemulsion adjuvant formulations manufactured with the synthetic poly(isoprene) material are evaluated in comparison to emulsions made with shark-derived squalene. Emulsions containing the synthetic poly(isoprene) achieved smaller particle size and equivalent or enhanced bioactivity (stimulation of cytokine production in human whole blood) compared to corresponding shark squalene emulsions. However, as opposed to the shark squalene-based emulsions, the poly(isoprene) emulsions demonstrated reduced long-term size stability and induced hemolysis at high concentrations. Finally, we demonstrate that the synthetic oligomeric poly(isoprene) material could successfully be hydrogenated such that >95% of the double bonds were successfully removed to give a representative poly(isoprene)-derived squalane mimic.
Synthetic Morphogenesis.

PubMed

Teague, Brian P; Guye, Patrick; Weiss, Ron

2016-09-01

Throughout biology, function is intimately linked with form. Across scales ranging from subcellular to multiorganismal, the identity and organization of a biological structure's subunits dictate its properties. The field of molecular morphogenesis has traditionally been concerned with describing these links, decoding the molecular mechanisms that give rise to the shape and structure of cells, tissues, organs, and organisms. Recent advances in synthetic biology promise unprecedented control over these molecular mechanisms; this opens the path to not just probing morphogenesis but directing it. This review explores several frontiers in the nascent field of synthetic morphogenesis, including programmable tissues and organs, synthetic biomaterials and programmable matter, and engineering complex morphogenic systems de novo. We will discuss each frontier's objectives, current approaches, constraints and challenges, and future potential. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

A diapycnal diffusivity model for stratified environmental flows

NASA Astrophysics Data System (ADS)

Bouffard, Damien; Boegman, Leon

2013-06-01

The vertical diffusivity of density, Kρ, regulates ocean circulation, climate and coastal water quality. Kρ is difficult to measure and model in these stratified turbulent flows, resulting in the need for the development of Kρ parameterizations from more readily measurable flow quantities. Typically, Kρ is parameterized from turbulent temperature fluctuations using the Osborn-Cox model or from the buoyancy frequency, N, kinematic viscosity, ν, and the rate of dissipation of turbulent kinetic energy, ɛ, using the Osborn model. More recently, Shih et al. (2005, J. Fluid Mech. 525: 193-214) proposed a laboratory scale parameterization for Kρ, at Prandtl number (ratio of the viscosity over the molecular diffusivity) Pr = 0.7, in terms of the turbulence intensity parameter, Re=ɛ/(νN), which is the ratio between the destabilizing effect of turbulence to the stabilizing effects of stratification and viscosity. In the present study, we extend the SKIF parameterization, against extensive sets of published data, over 0.7 < Pr < 700 and validate it at field scale. Our results show that the SKIF model must be modified to include a new Buoyancy-controlled mixing regime, between the Molecular and Transitional regimes, where Kρ is captured using the molecular diffusivity and Osborn model, respectively. The Buoyancy-controlled regime occurs over 10Pr
Influence of fluid viscosity and wetting on multiscale viscoelastic lubrication in soft tribological contacts.

PubMed

Selway, Nichola; Chan, Vincent; Stokes, Jason R

2017-02-22

Friction (and lubrication) between soft contacts is prevalent in many natural and engineered systems and plays a crucial role in determining their functionality. The contribution of viscoelastic hysteresis losses to friction in these systems has been well-established and defined for dry contacts; however, the influence of fluid viscosity and wetting on these components of friction has largely been overlooked. We provide systematic experimental evidence of the influence of lubricant viscosity and wetting on lubrication across multiple regimes within a viscoelastic contact. These effects are investigated for comparatively smooth and rough elastomeric contacts (PTFE-PDMS and PDMS-PDMS) lubricated by a series of Newtonian fluids with systematically controlled viscosity and static wetting properties, using a ball-on-disc tribometer. The distinct tribological behaviour, characterised generally by a decrease in the friction coefficient with increasing fluid viscosity and wettability, is explained in terms of lubricant dewetting and squeeze-out dynamics and their impact on multi-scale viscoelastic dissipation mechanisms at the bulk-, asperity-, sub-asperity- and molecular-scale. It is proposed that lubrication within the (non-molecularly) smooth contact is governed by localised fluid entrapment and molecular-scale (interfacial) viscoelastic effects, while additional rubber hysteresis stimulated by fluid-asperity interactions, combined with rapid fluid drainage at low speeds within the rough contact, alter the general shape of the Stribeck curve. This fluid viscosity effect is in some agreement with theoretical predictions. Conventional methods for analysing and interpreting tribological data, which typically involve scaling sliding velocity with lubricant viscosity, need to be revised for viscoelastic contacts with consideration of these indirect viscosity effects.
Stability investigations of relaxing molecular gas flows. Results and perspectives

NASA Astrophysics Data System (ADS)

Grigor'ev, Yurii N.; Ershov, Igor V.

2017-10-01

This article presents results of systematic investigations of a dissipative effect which manifests itself as the growth of hydrodynamic stability and suppression of turbulence in relaxing molecular gas flows. The effect can be a new way for control stability and laminar turbulent transition in aerodynamic flows. The consideration of suppression of inviscid acoustic waves in 2D shear flows is presented. Nonlinear evolution of large-scale vortices and Kelvin — Helmholtz waves in relaxing shear flows are studied. Critical Reynolds numbers in supersonic Couette flows are calculated analytically and numerically within the framework of both classical linear and nonlinear energy hydrodynamic stability theories. The calculations clearly show that the relaxation process can appreciably delay the laminar-turbulent transition. The aim of this article is to show the new dissipative effect, which can be used for flow control and laminarization.
Multiscale computational modeling reveals a critical role for TNF-α receptor 1 dynamics in tuberculosis granuloma formation.

PubMed

Fallahi-Sichani, Mohammad; El-Kebir, Mohammed; Marino, Simeone; Kirschner, Denise E; Linderman, Jennifer J

2011-03-15

Multiple immune factors control host responses to Mycobacterium tuberculosis infection, including the formation of granulomas, which are aggregates of immune cells whose function may reflect success or failure of the host to contain infection. One such factor is TNF-α. TNF-α has been experimentally characterized to have the following activities in M. tuberculosis infection: macrophage activation, apoptosis, and chemokine and cytokine production. Availability of TNF-α within a granuloma has been proposed to play a critical role in immunity to M. tuberculosis. However, in vivo measurement of a TNF-α concentration gradient and activities within a granuloma are not experimentally feasible. Further, processes that control TNF-α concentration and activities in a granuloma remain unknown. We developed a multiscale computational model that includes molecular, cellular, and tissue scale events that occur during granuloma formation and maintenance in lung. We use our model to identify processes that regulate TNF-α concentration and cellular behaviors and thus influence the outcome of infection within a granuloma. Our model predicts that TNF-αR1 internalization kinetics play a critical role in infection control within a granuloma, controlling whether there is clearance of bacteria, excessive inflammation, containment of bacteria within a stable granuloma, or uncontrolled growth of bacteria. Our results suggest that there is an interplay between TNF-α and bacterial levels in a granuloma that is controlled by the combined effects of both molecular and cellular scale processes. Finally, our model elucidates processes involved in immunity to M. tuberculosis that may be new targets for therapy.
Transport in Physical Space: The Example of Pedestrians, Cars, and Molecular Motors

NASA Astrophysics Data System (ADS)

Appert-Rolland, Cécile; Klein, Sarah; Ebbinghaus, Maximilian; Santen, Ludger

Transport systems in physical space exhibit various phenomena which may have some counterparts in socio- or econo-systems. We review here several of them. In highway vehicular traffic, the introduction of a reaction time leads to metastability and hysteresis. Pattern formation occurs in pedestrian flows. At a microscopic scale, we can learn from molecular pedestrians that transporting an object by opposite teams can be more efficient in a crowded environment and allow for an easy control of the system. Besides, we will show that the interplay between transport and the dynamics of the underlying network can sometimes lead to positive effects in terms of efficiency of transport.
Microscopic origin of electric-field-induced modulation of Curie temperature in cobalt

NASA Astrophysics Data System (ADS)

Ando, Fuyuki; Yamada, Kihiro T.; Koyama, Tomohiro; Ishibashi, Mio; Shiota, Yoichi; Moriyama, Takahiro; Chiba, Daichi; Ono, Teruo

2018-07-01

The Curie temperature T C is one of the most fundamental physical properties of ferromagnetic materials and can be described by the Weiss molecular field theory with the exchange interaction of neighboring atoms. Here, we demonstrate the electrical control of exchange coupling in cobalt films through direct magnetization measurements. We find that the reduction in magnetization with temperature, which is caused by thermal spin wave excitation and scales with Bloch’s law, clearly depends on the applied electric field. Furthermore, we confirm that the correlation between the electric-field-induced modulation of T C and that of exchange coupling follows the Weiss molecular field theory.
Star Formation: Answering Fundamental Questions During the Spitzer Warm Mission Phase

NASA Astrophysics Data System (ADS)

Strom, Steve; Allen, Lori; Carpenter, John; Hartmann, Lee; Megeath, S. Thomas; Rebull, Luisa; Stauffer, John R.; Liu, Michael

2007-10-01

Through existing studies of star-forming regions, Spitzer has created rich databases which have already profoundly influenced our ability to understand the star and planet formation process on micro and macro scales. However, it is essential to note that Spitzer observations to date have focused largely on deep observations of regions of recent star formation associated directly with well-known molecular clouds located within 500 pc. What has not been done is to explore to sufficient depth or breadth a representative sample of the much larger regions surrounding the more massive of these molecular clouds. Also, while there have been targeted studies of specific distant star forming regions, in general, there has been little attention devoted to mapping and characterizing the stellar populations and star-forming histories of the surrounding giant molecular clouds (GMCs). As a result, we have yet to develop an understanding of the major physical processes that control star formation on the scale or spiral arms. Doing so will allow much better comparison of star-formation in our galaxy to the star-forming complexes that dominate the spiral arms of external galaxies. The power of Spitzer in the Warm Mission for studies of star formation is its ability to carry out large-scale surveys unbiased by prior knowledge of ongoing star formation or the presence of molecular clouds. The Spitzer Warm Mission will provide two uniquely powerful capabilities that promise equally profound advances : high sensitivity and efficient coverage of many hundreds of square degrees, and angular resolution sufficient to resolve dense groups and clusters of YSOs and to identify contaminating background galaxies whose colors mimic those of young stars. In this contribution, we describe two major programs: a survey of the outer regions of selected nearby OB associations, and a study of distant GMCs and star formation on the scale of a spiral arm.
MD Simulation on Collision Behavior Between Nano-Scale TiO₂ Particles During Vacuum Cold Spraying.

PubMed

Yao, Hai-Long; Yang, Guan-Jun; Li, Chang-Jiu

2018-04-01

Particle collision behavior influences significantly inter-nano particle bonding formation during the nano-ceramic coating deposition by vacuum cold spraying (or aerosol deposition method). In order to illuminate the collision behavior between nano-scale ceramic particles, molecular dynamic simulation was applied to explore impact process between nano-scale TiO2 particles through controlling impact velocities. Results show that the recoil efficiency of the nano-scale TiO2 particle is decreased with the increase of the impact velocity. Nano-scale TiO2 particle exhibits localized plastic deformation during collision at low velocities, while it is intensively deformed by collision at high velocities. This intensive deformation promotes the nano-particle adhesion rather than rebounding off. A relationship between the adhesion energy and the rebound energy is established for the bonding formation of the nano-scale TiO2 particle. The adhesion energy required to the bonding formation between nano-scale ceramic particles can be produced by high velocity collision.
Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

PubMed

Cawkwell, M J; Niklasson, Anders M N

2012-10-07

Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.
Consequences of Molecular-Scale Non-Equilibrium Activity on the Dynamics and Mechanics of Self-Assembled Actin-Based Structures and Materials

NASA Astrophysics Data System (ADS)

Marshall Mccall, Patrick

Living cells are hierarchically self-organized forms of active soft matter: molecules on the nanometer scale form functional structures and organelles on the micron scale, which then compose cells on the scale of 10s of microns. While the biological functions of intracellular organelles are defined by the composition and properties of the structures themselves, how those bulk properties emerge from the properties and interactions of individual molecules remains poorly understood. Actin, a globular protein which self-assembles into dynamic semi-flexible polymers, is the basic structural material of cells and the major component of many functional organelles. In this thesis, I have used purified actin as a model system to explore the interplay between molecular-scale dynamics and organelle-scale functionality, with particular focus on the role of molecular-scale non-equilibrium activity. One of the most canonical forms of molecular-scale non-equilibrium activity is that of mechanoenzymes, also called motor proteins. These proteins utilized the free energy liberated by hydrolysis of ATP to perform mechanical work, thereby introducing non-equilibrium "active" stresses on the molecular scale. Combining experiments with mathematical modeling, we demonstrate in this thesis that non-equilibrium motor activity is sufficient to drive self-organization and pattern formation of the multimeric actin-binding motor protein Myosin II on 1D reconstituted actomyosin bundles. Like myosin, actin is itself an ATPase. However, nono-equilibrium ATP hydrolysis on actin is known to regulate the stability and assembly kinetics of actin filaments rather than generate active stresses per se. At the level of single actin filaments, the inhomogeneous nucleotide composition generated along the filament length by hydrolysis directs binding of regulatory proteins like cofilin, which mediate filament disassembly and thereby accelerate actin filament turnover. The concequences of this non-equilibrium turnover on the steady-state properties of collections of filaments remained unclear. Here, I reconstituted tunable, non-equilibrium actin turnover dynamics in entangled solutions of actin filaments as a model of the actin cortex of living cells. We found that this non-equilibrium turnover decouples solution mechanics from microstructure, enabling structurally indistinguishable materials to behave effectively as either viscous fluids or elastic gels. Additionally, we employed computer simulations to identify the dynamical regime in which actin turnover controls the effective viscosity of 2D cross-linked actin networks in the presence of motors. Additionally, I examine in this thesis the localization and self-assembly of actin filaments in condensed liquid phases called polyelectrolyte coacervates as a model membrane-less organelle. We find that concentration of actin through spontaneous partitioning preferentially to the coacervate phase accelerates the assembly of filaments. These filaments then localize to the coacervate-bulk interface, generating particles with visco-elastic shells surrounding liquid cores. In this case, the properties of the condensed phase enable regulation of actin assembly dynamics.
On the strong influence of molecular interactions over large distances

NASA Astrophysics Data System (ADS)

Pfennig, Andreas

2018-03-01

Molecular-dynamics simulations of liquid water show deterministic chaos, i.e. an intentionally introduced molecular position shift of an individual molecule increases exponentially by a factor of 10 in 0.23 ps. This is a Lyaponov instability. As soon as it reaches molecular scale, the direction of the resulting shift in molecular motions is unpredictable. The influence of any individual distant particle on an observed molecule will be minute, but the effect will quickly increase to molecular scale and beyond due to this exponential growth. Consequently, any individual particle in the universe will affect the behavior of any molecule within at most 33 ps after the interaction reaches it. A larger distance of the faraway particle does not decrease the influence on an observed molecule, but the effect reaches molecular scale only some ps later. Thus in evaluating the interactions, nearby and faraway molecules have to be equally accounted for. The consequences of this quickly reacting network of interactions on universal scale are fundamental. Even in a strictly deterministic view, molecular behavior is principally unpredictable, and thus has to be regarded random. Corresponding statements apply for any particles interacting. This result leads to a fundamental rethinking of the structure of interactions of molecules and particles as well as the behavior of reality.
Understanding physicochemical properties changes from multi-scale structures of starch/CNT nanocomposite films.

PubMed

Liu, Siyuan; Li, Xiaoxi; Chen, Ling; Li, Lin; Li, Bing; Zhu, Jie

2017-11-01

From the view of multi-scale structures of hydroxypropyl starch (HPS)/carbon nanotube (CNT) nanocomposite films, the film physicochemical properties were affected by comprehensive factors including molecular interaction, short range molecular conformation, crystalline structure and aggregated structure. The less original HPS hydrogen bonding that was broken, less decreased order of HPS short range molecular conformation, lower film crystallinity and larger size of micro-ordered regions contributed to higher tensile strength and Young's modulus of the film with CNT content of 0.5% (g/g, CNT in HPS). The higher film overall crystallinity and larger size of micro-ordered regions of the film with CNT content of 0.05%-0.3% compared with those of control contributed to better film barrier property. The addition of CNT with the content of 0.05%-0.5% broke the original HPS hydrogen bonding and decreased the order of starch short range molecular conformation, which counteracted the positive effect of CNT on the thermal stability of the material, thus thermal degradation temperature of these nanocomposite films did not increase. But the sharp increase of film crystallinity increased film thermal degradation temperature. This study provided a better understanding of film physicochemical properties changes which guides to rational design of starch-based nanocomposite films for packaging and coating application. Copyright © 2017. Published by Elsevier B.V.
Simulations of molecular self-assembled monolayers on surfaces: packing structures, formation processes and functions tuned by intermolecular and interfacial interactions.

PubMed

Wen, Jin; Li, Wei; Chen, Shuang; Ma, Jing

2016-08-17

Surfaces modified with a functional molecular monolayer are essential for the fabrication of nano-scale electronics or machines with novel physical, chemical, and/or biological properties. Theoretical simulation based on advanced quantum chemical and classical models is at present a necessary tool in the development, design, and understanding of the interfacial nanostructure. The nanoscale surface morphology, growth processes, and functions are controlled by not only the electronic structures (molecular energy levels, dipole moments, polarizabilities, and optical properties) of building units but also the subtle balance between intermolecular and interfacial interactions. The switchable surfaces are also constructed by introducing stimuli-responsive units like azobenzene derivatives. To bridge the gap between experiments and theoretical models, opportunities and challenges for future development of modelling of ferroelectricity, entropy, and chemical reactions of surface-supported monolayers are also addressed. Theoretical simulations will allow us to obtain important and detailed information about the structure and dynamics of monolayer modified interfaces, which will guide the rational design and optimization of dynamic interfaces to meet challenges of controlling optical, electrical, and biological functions.
Designed synthesis and supramolecular architectures of furan-substituted perylene diimide.

PubMed

Yu, Yanwen; Li, Yongjun; Qin, Zhihong; Jiang, Runsheng; Liu, Huibiao; Li, Yuliang

2013-06-01

Novel furan-substituted perylene diimides are successfully synthesized and an efficient supramolecular architecture approach to construct zero/one-dimensional nano- and micro-structures by controlling solvents has been demonstrated. The aggregate structure conversion in different molecular structures can be controlled in the form of sphere-like, rod-like, and vesicle-like structures. As expected, these solid supramolecular rod-like architectures displayed interesting optical waveguide behavior, which indicates the aggregate structure materials of furan-substituted perylene diimides have the potential application as micro-scale photonic elements. Copyright © 2013 Elsevier Inc. All rights reserved.
Attosecond-recollision-controlled selective fragmentation of polyatomic molecules.

PubMed

Xie, Xinhua; Doblhoff-Dier, Katharina; Roither, Stefan; Schöffler, Markus S; Kartashov, Daniil; Xu, Huailiang; Rathje, Tim; Paulus, Gerhard G; Baltuška, Andrius; Gräfe, Stefanie; Kitzler, Markus

2012-12-14

Control over various fragmentation reactions of a series of polyatomic molecules (acetylene, ethylene, 1,3-butadiene) by the optical waveform of intense few-cycle laser pulses is demonstrated experimentally. We show both experimentally and theoretically that the responsible mechanism is inelastic ionization from inner-valence molecular orbitals by recolliding electron wave packets, whose recollision energy in few-cycle ionizing laser pulses strongly depends on the optical waveform. Our work demonstrates an efficient and selective way of predetermining fragmentation and isomerization reactions in polyatomic molecules on subfemtosecond time scales.
Thermodynamic metrics and optimal paths.

PubMed

Sivak, David A; Crooks, Gavin E

2012-05-11

A fundamental problem in modern thermodynamics is how a molecular-scale machine performs useful work, while operating away from thermal equilibrium without excessive dissipation. To this end, we derive a friction tensor that induces a Riemannian manifold on the space of thermodynamic states. Within the linear-response regime, this metric structure controls the dissipation of finite-time transformations, and bestows optimal protocols with many useful properties. We discuss the connection to the existing thermodynamic length formalism, and demonstrate the utility of this metric by solving for optimal control parameter protocols in a simple nonequilibrium model.
Dynamics of light-field control of molecular dissociation at the few-cycle limit.

PubMed

Tong, X M; Lin, C D

2007-03-23

We studied the laser-molecule interaction dynamics that leads to the asymmetric D+ ion ejection in the dissociative ionization of D2 molecules observed recently in Kling et al. [Science 312, 246 (2006)10.1126/science.1126259]. By changing the carrier-envelope phase, we showed that the asymmetry is a consequence of manipulating the initial ionization and the rescattering of the electrons within one optical cycle of the laser. The result illustrates the feasibility of coherent control of reaction dynamics at the attosecond time scale.
Multiscale diffusion of a molecular probe in a crowded environment: a concept

NASA Astrophysics Data System (ADS)

Currie, Megan; Thao, Chang; Timerman, Randi; Welty, Robb; Berry, Brenden; Sheets, Erin D.; Heikal, Ahmed A.

2015-08-01

Living cells are crowded with macromolecules and organelles. Yet, it is not fully understood how macromolecular crowding affects the myriad of biochemical reactions, transport and the structural stability of biomolecules that are essential to cellular function and survival. These molecular processes, with or without electrostatic interactions, in living cells are therefore expected to be distinct from those carried out in test tube in dilute solutions where excluded volumes are absent. Thus there is an urgent need to understand the macromolecular crowding effects on cellular and molecular biophysics towards quantitative cell biology. In this report, we investigated how biomimetic crowding affects both the rotational and translation diffusion of a small probe (rhodamine green, RhG). For biomimetic crowding agents, we used Ficoll-70 (synthetic polymer), bovine serum albumin and ovalbumin (proteins) at various concentrations in a buffer at room temperature. As a control, we carried out similar measurements on glycerolenriched buffer as an environment with homogeneous viscosity as a function of glycerol concentration. The corresponding bulk viscosity was measured independently to test the validity of the Stokes-Einstein model of a diffusing species undergoing a random walk. For rotational diffusion (ps-ns time scale), we used time-resolved anisotropy measurements to examine potential binding of RhG as a function of the crowding agents (surface structure and size). For translational diffusion (μs-s time scale), we used fluorescence correlation spectroscopy for single-molecule fluctuation analysis. Our results allow us to examine the diffusion model of a molecular probe in crowded environments as a function of concentration, length scale, homogeneous versus heterogeneous viscosity, size and surface structures. These biomimetic crowding studies, using non-invasive fluorescence spectroscopy methods, represent an important step towards understanding cellular biophysics and quantitative cell biology.
Molecular-Scale Features that Govern the Effects of O-Glycosylation on a Carbohydrate-Binding Module

DOE PAGES

Guan, Xiaoyang; Chaffey, Patrick K.; Zeng, Chen; ...

2015-09-21

The protein glycosylation is a ubiquitous post-translational modification in all kingdoms of life. Despite its importance in molecular and cellular biology, the molecular-level ramifications of O-glycosylation on biomolecular structure and function remain elusive. Here, we took a small model glycoprotein and changed the glycan structure and size, amino acid residues near the glycosylation site, and glycosidic linkage while monitoring any corresponding changes to physical stability and cellulose binding affinity. The results of this study reveal the collective importance of all the studied features in controlling the most pronounced effects of O-glycosylation in this system. This study suggests the possibility ofmore » designing proteins with multiple improved properties by simultaneously varying the structures of O-glycans and amino acids local to the glycosylation site.« less
Single-molecule quantum dot as a Kondo simulator

NASA Astrophysics Data System (ADS)

Hiraoka, R.; Minamitani, E.; Arafune, R.; Tsukahara, N.; Watanabe, S.; Kawai, M.; Takagi, N.

2017-06-01

Structural flexibility of molecule-based systems is key to realizing the novel functionalities. Tuning the structure in the atomic scale enables us to manipulate the quantum state in the molecule-based system. Here we present the reversible Hamiltonian manipulation in a single-molecule quantum dot consisting of an iron phthalocyanine molecule attached to an Au electrode and a scanning tunnelling microscope tip. We precisely controlled the position of Fe2+ ion in the molecular cage by using the tip, and tuned the Kondo coupling between the molecular spins and the Au electrode. Then, we realized the crossover between the strong-coupling Kondo regime and the weak-coupling regime governed by spin-orbit interaction in the molecule. The results open an avenue to simulate low-energy quantum many-body physics and quantum phase transition through the molecular flexibility.

Molecular-Scale Electronics: From Concept to Function.

PubMed

Xiang, Dong; Wang, Xiaolong; Jia, Chuancheng; Lee, Takhee; Guo, Xuefeng

2016-04-13

Creating functional electrical circuits using individual or ensemble molecules, often termed as "molecular-scale electronics", not only meets the increasing technical demands of the miniaturization of traditional Si-based electronic devices, but also provides an ideal window of exploring the intrinsic properties of materials at the molecular level. This Review covers the major advances with the most general applicability and emphasizes new insights into the development of efficient platform methodologies for building reliable molecular electronic devices with desired functionalities through the combination of programmed bottom-up self-assembly and sophisticated top-down device fabrication. First, we summarize a number of different approaches of forming molecular-scale junctions and discuss various experimental techniques for examining these nanoscale circuits in details. We then give a full introduction of characterization techniques and theoretical simulations for molecular electronics. Third, we highlight the major contributions and new concepts of integrating molecular functionalities into electrical circuits. Finally, we provide a critical discussion of limitations and main challenges that still exist for the development of molecular electronics. These analyses should be valuable for deeply understanding charge transport through molecular junctions, the device fabrication process, and the roadmap for future practical molecular electronics.
Molecular machines open cell membranes

NASA Astrophysics Data System (ADS)

García-López, Víctor; Chen, Fang; Nilewski, Lizanne G.; Duret, Guillaume; Aliyan, Amir; Kolomeisky, Anatoly B.; Robinson, Jacob T.; Wang, Gufeng; Pal, Robert; Tour, James M.

2017-08-01

Beyond the more common chemical delivery strategies, several physical techniques are used to open the lipid bilayers of cellular membranes. These include using electric and magnetic fields, temperature, ultrasound or light to introduce compounds into cells, to release molecular species from cells or to selectively induce programmed cell death (apoptosis) or uncontrolled cell death (necrosis). More recently, molecular motors and switches that can change their conformation in a controlled manner in response to external stimuli have been used to produce mechanical actions on tissue for biomedical applications. Here we show that molecular machines can drill through cellular bilayers using their molecular-scale actuation, specifically nanomechanical action. Upon physical adsorption of the molecular motors onto lipid bilayers and subsequent activation of the motors using ultraviolet light, holes are drilled in the cell membranes. We designed molecular motors and complementary experimental protocols that use nanomechanical action to induce the diffusion of chemical species out of synthetic vesicles, to enhance the diffusion of traceable molecular machines into and within live cells, to induce necrosis and to introduce chemical species into live cells. We also show that, by using molecular machines that bear short peptide addends, nanomechanical action can selectively target specific cell-surface recognition sites. Beyond the in vitro applications demonstrated here, we expect that molecular machines could also be used in vivo, especially as their design progresses to allow two-photon, near-infrared and radio-frequency activation.
Molecular machines open cell membranes.

PubMed

García-López, Víctor; Chen, Fang; Nilewski, Lizanne G; Duret, Guillaume; Aliyan, Amir; Kolomeisky, Anatoly B; Robinson, Jacob T; Wang, Gufeng; Pal, Robert; Tour, James M

2017-08-30

Beyond the more common chemical delivery strategies, several physical techniques are used to open the lipid bilayers of cellular membranes. These include using electric and magnetic fields, temperature, ultrasound or light to introduce compounds into cells, to release molecular species from cells or to selectively induce programmed cell death (apoptosis) or uncontrolled cell death (necrosis). More recently, molecular motors and switches that can change their conformation in a controlled manner in response to external stimuli have been used to produce mechanical actions on tissue for biomedical applications. Here we show that molecular machines can drill through cellular bilayers using their molecular-scale actuation, specifically nanomechanical action. Upon physical adsorption of the molecular motors onto lipid bilayers and subsequent activation of the motors using ultraviolet light, holes are drilled in the cell membranes. We designed molecular motors and complementary experimental protocols that use nanomechanical action to induce the diffusion of chemical species out of synthetic vesicles, to enhance the diffusion of traceable molecular machines into and within live cells, to induce necrosis and to introduce chemical species into live cells. We also show that, by using molecular machines that bear short peptide addends, nanomechanical action can selectively target specific cell-surface recognition sites. Beyond the in vitro applications demonstrated here, we expect that molecular machines could also be used in vivo, especially as their design progresses to allow two-photon, near-infrared and radio-frequency activation.
Probing the brain with molecular fMRI.

PubMed

Ghosh, Souparno; Harvey, Peter; Simon, Jacob C; Jasanoff, Alan

2018-06-01

One of the greatest challenges of modern neuroscience is to incorporate our growing knowledge of molecular and cellular-scale physiology into integrated, organismic-scale models of brain function in behavior and cognition. Molecular-level functional magnetic resonance imaging (molecular fMRI) is a new technology that can help bridge these scales by mapping defined microscopic phenomena over large, optically inaccessible regions of the living brain. In this review, we explain how MRI-detectable imaging probes can be used to sensitize noninvasive imaging to mechanistically significant components of neural processing. We discuss how a combination of innovative probe design, advanced imaging methods, and strategies for brain delivery can make molecular fMRI an increasingly successful approach for spatiotemporally resolved studies of diverse neural phenomena, perhaps eventually in people. Copyright © 2018 Elsevier Ltd. All rights reserved.
Controllable growth of layered selenide and telluride heterostructures and superlattices using molecular beam epitaxy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vishwanath, Suresh; Liu, Xinyu; Rouvimov, Sergei

2016-01-06

Layered materials are an actively pursued area of research for realizing highly scaled technologies involving both traditional device structures as well as new physics. Lately, non-equilibrium growth of 2D materials using molecular beam epitaxy (MBE) is gathering traction in the scientific community and here we aim to highlight one of its strengths, growth of abrupt heterostructures, and superlattices (SLs). In this work we present several of the firsts: first growth of MoTe 2 by MBE, MoSe 2 on Bi 2Se 3 SLs, transition metal dichalcogenide (TMD) SLs, and lateral junction between a quintuple atomic layer of Bi 2Te 3 andmore » a triple atomic layer of MoTe 2. In conclusion, reflected high electron energy diffraction oscillations presented during the growth of TMD SLs strengthen our claim that ultrathin heterostructures with monolayer layer control is within reach.« less
Multifunctional-layered materials for creating membrane-restricted nanodomains and nanoscale imaging

NASA Astrophysics Data System (ADS)

Srinivasan, P.

2016-01-01

Experimental platform that allows precise spatial positioning of biomolecules with an exquisite control at nanometer length scales is a valuable tool to study the molecular mechanisms of membrane bound signaling. Using micromachined thin film gold (Au) in layered architecture, it is possible to add both optical and biochemical functionalities in in vitro. Towards this goal, here, I show that docking of complementary DNA tethered giant phospholiposomes on Au surface can create membrane-restricted nanodomains. These nanodomains are critical features to dissect molecular choreography of membrane signaling complexes. The excited surface plasmon resonance modes of Au allow label-free imaging at diffraction-limited resolution of stably docked DNA tethered phospholiposomes, and lipid-detergent bicelle structures. Such multifunctional building block enables realizing rigorously controlled in vitro set-up to model membrane anchored biological signaling, besides serving as an optical tool for nanoscale imaging.
[Control of craving for methamphetamine: development of scales for dependence and search for medicines for treatment].

PubMed

Ogai, Yasukazu; Haraguchi, Ayako; Kondo, Ayumi; Takamatsu, Yukio; Yamamoto, Hideko; Sendoo, Eiichi; Ikeda, Katzutaka

2005-10-01

Methamphetamine dependence presents a serious problem not only for patients but also for society. Medical treatment has mainly targeted psychotic symptoms such as hallucination and delusion, and ignored the symptoms of craving, which are the major cause of dependence. Therefore, the risk of lapse into methamphetamine reuse remains very high. Although development of both medicines and programs for treatment of craving is needed, progress has been hampered by the lack of appropriate scales for assessing the severity of dependence and craving. On the other hand, recent breakthroughs in genomic sciences and molecular medicine have made it possible to investigate the molecular mechanisms underlying craving in animals. This paper reviews studies on the development of scales for assessing the severity of methamphetamine dependence and craving, together with recent data on candidate medicines for craving treatment in animals. The reliability and validity of the revised Addiction Severity Index -Japanese version (ASI-J) was confirmed after its administration to 100 drug abuse patients. The Craving Index was also newly developed, and its validity for prediction of relapse was confirmed. In animal experiments, fluoxetine, a selective serotonin reuptake inhibitor, was recognized as a candidate medicine for treatment of methamphetamine dependence.
Atomic structure of water/Au, Ag, Cu and Pt atomic junctions.

PubMed

Li, Yu; Kaneko, Satoshi; Fujii, Shintaro; Nishino, Tomoaki; Kiguchi, Manabu

2017-02-08

Much progress has been made in understanding the transport properties of atomic-scale conductors. We prepared atomic-scale metal contacts of Cu, Ag, Au and Pt using a mechanically controllable break junction method at 10 K in a cryogenic vacuum. Water molecules were exposed to the metal atomic contacts and the effect of molecular adsorption was investigated by electronic conductance measurements. Statistical analysis of the electronic conductance showed that the water molecule(s) interacted with the surface of the inert Au contact and the reactive Cu ant Pt contacts, where molecular adsorption decreased the electronic conductance. A clear conductance signature of water adsorption was not apparent at the Ag contact. Detailed analysis of the conductance behaviour during a contact-stretching process indicated that metal atomic wires were formed for the Au and Pt contacts. The formation of an Au atomic wire consisting of low coordination number atoms leads to increased reactivity of the inert Au surface towards the adsorption of water.
Effects of nanoscale aggregation on mechanical properties and local dynamics of precise acid- and ion-containing polymers

NASA Astrophysics Data System (ADS)

Middleton, Luri Robert

Acid- and ion-containing polymers have interchain interactions that alter polymer behavior at the nano, micro, and bulk length scales. Strong secondary-bonds act as thermo-reversible physical crosslinks between chains which drive self-assembly. Tuning theses interactions can modify bulk polymer properties including stiffness, toughness, melt viscosity, resilience, clarity, abrasion resistance and puncture resistance. Furthermore, understanding and improving the relevant factors that control transport properties would have vast implications on developing solid polymer electrolytes (SPEs) for technologically important applications including water desalination, ion exchange membranes and microelectronics. This thesis explores the structure - processing - morphology - property relationships of acid and ionic functionalized polymers. Improvements in synthetic techniques and advancements in characterization methods have enabled new studies of associating polymer systems. Synthesis of entangled, high molecular weight, linear polyethylene (PE) chains functionalized with interacting pendant groups (acidic or ionic) placed periodically along the polymer backbone represent a new class of associating polymers. These polymers with periodic distributions of acid groups are much more homogenous than the commercially available polymers. Previous studies of these polymers with greater structural homogeneity revealed great variety in morphologies of the nano-aggregated polar groups within the non-polar polymer matrix. This thesis correlated the morphologies with bulk properties through real-time X-ray scattering and tensile deformation at a range of temperatures and sample compositions. New, transient morphologies and hierarchical morphologies were observed which coincided with unusual tensile strain hardening. These results indicate that improvements in synthetic control of polymers can enhance physical properties such as tensile strain-hardening, through cooperative bonding between chains. The structural regularity of precise polyethylenes also enables robust comparisons between experiments and computer simulations. At pico- to nano-seconds time scales and length scales of polymer and aggregate dynamics, neutron scattering and molecular dynamics simulations were combined to extend the knowledge of the molecular-level aggregated polymer dynamics. These experiments provide a baseline for future studies of ion-conduction in associating polymer melts.
Molecular and morphological identification of pistachio armored scale insects (Hemiptera: Diaspididae), with description of a new species.

PubMed

Hosseininaveh, Fatemeh; Nozari, Jamasb; Kaydan, Mehmet Bora; Hosseininaveh, Vahid

2016-12-01

Members of the family Diaspididae (Hemiptera: Coccomorpha) can be devastating pests that suck parenchyma cell contents from crops and cause severe damage to pistachio trees (Pistacia vera L.). The current research collected and characterized diaspidid species from pistachio orchards in Kerman province, Iran, according to their morphological and molecular features. Lepidosaphes pistaciae Archangelskaya, Suturaspis davatchi (Balachowsky & Kaussari) and Melanaspis inopinata (Leonardi) are redescribed and a new species, Melanaspis pistaciae Hosseininaveh & Kaydan sp. n., is described. Phylogenetic trees based on molecular analysis of COI and 28S rDNA fragments placed all the species in separated clades and confirmed M. pistaciae as a new taxon which is concluded by morphological differences. Molecular analysis suggests non-monophyly of the populations of each species. Melanaspis pistaciae sp. n. has spread to most cultivated pistachio areas in Iran and has probably been misidentified as M. inopinata in the past. Further investigation of the biology of this species may lead to development of more effective approaches for controlling this pest.
Computational and Experimental Investigations of the Molecular Scale Structure and Dynamics of Gologically Important Fluids and Mineral-Fluid Interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bowers, Geoffrey

United States Department of Energy grant DE-FG02-10ER16128, “Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces” (Geoffrey M. Bowers, P.I.) focused on developing a molecular-scale understanding of processes that occur in fluids and at solid-fluid interfaces using the combination of spectroscopic, microscopic, and diffraction studies with molecular dynamics computer modeling. The work is intimately tied to the twin proposal at Michigan State University (DOE DE-FG02-08ER15929; same title: R. James Kirkpatrick, P.I. and A. Ozgur Yazaydin, co-P.I.).
Characterization via atomic force microscopy of discrete plasticity in collagen fibrils from mechanically overloaded tendons: Nano-scale structural changes mimic rope failure.

PubMed

Baldwin, Samuel J; Kreplak, Laurent; Lee, J Michael

2016-07-01

Tendons exposed to tensile overload show a structural alteration at the fibril scale termed discrete plasticity. Serial kinks appear along individual collagen fibrils that are susceptible to enzymatic digestion and are thermally unstable. Using atomic force microscopy we mapped the topography and mechanical properties in dehydrated and hydrated states of 25 control fibrils and 25 fibrils displaying periodic kinks, extracted from overloaded bovine tail tendons. Using the measured modulus of the hydrated fibrils as a probe of molecular density, we observed a non-linear negative correlation between molecular density and kink density of individual fibrils. This is accompanied by an increase in water uptake with kink density and a doubling of the coefficient of variation of the modulus between kinked, and control fibrils. The mechanical property maps of kinked collagen fibrils show radial heterogeneity that can be modeled as a high-density core surrounded by a low-density shell. The core of the fibril contains the kink structures characteristic of discrete plasticity; separated by inter-kink regions, which often retain the D-banding structure. We propose that the shell and kink structures mimic characteristic damage motifs observed in laid rope strands. Copyright © 2016 Elsevier Ltd. All rights reserved.
Time scale of diffusion in molecular and cellular biology

NASA Astrophysics Data System (ADS)

Holcman, D.; Schuss, Z.

2014-05-01

Diffusion is the driver of critical biological processes in cellular and molecular biology. The diverse temporal scales of cellular function are determined by vastly diverse spatial scales in most biophysical processes. The latter are due, among others, to small binding sites inside or on the cell membrane or to narrow passages between large cellular compartments. The great disparity in scales is at the root of the difficulty in quantifying cell function from molecular dynamics and from simulations. The coarse-grained time scale of cellular function is determined from molecular diffusion by the mean first passage time of molecular Brownian motion to a small targets or through narrow passages. The narrow escape theory (NET) concerns this issue. The NET is ubiquitous in molecular and cellular biology and is manifested, among others, in chemical reactions, in the calculation of the effective diffusion coefficient of receptors diffusing on a neuronal cell membrane strewn with obstacles, in the quantification of the early steps of viral trafficking, in the regulation of diffusion between the mother and daughter cells during cell division, and many other cases. Brownian trajectories can represent the motion of a molecule, a protein, an ion in solution, a receptor in a cell or on its membrane, and many other biochemical processes. The small target can represent a binding site or an ionic channel, a hidden active site embedded in a complex protein structure, a receptor for a neurotransmitter on the membrane of a neuron, and so on. The mean time to attach to a receptor or activator determines diffusion fluxes that are key regulators of cell function. This review describes physical models of various subcellular microdomains, in which the NET coarse-grains the molecular scale to a higher cellular-level, thus clarifying the role of cell geometry in determining subcellular function.
Re-membering the body: applications of computational neuroscience to the top-down control of regeneration of limbs and other complex organs.

PubMed

Pezzulo, G; Levin, M

2015-12-01

A major goal of regenerative medicine and bioengineering is the regeneration of complex organs, such as limbs, and the capability to create artificial constructs (so-called biobots) with defined morphologies and robust self-repair capabilities. Developmental biology presents remarkable examples of systems that self-assemble and regenerate complex structures toward their correct shape despite significant perturbations. A fundamental challenge is to translate progress in molecular genetics into control of large-scale organismal anatomy, and the field is still searching for an appropriate theoretical paradigm for facilitating control of pattern homeostasis. However, computational neuroscience provides many examples in which cell networks - brains - store memories (e.g., of geometric configurations, rules, and patterns) and coordinate their activity towards proximal and distant goals. In this Perspective, we propose that programming large-scale morphogenesis requires exploiting the information processing by which cellular structures work toward specific shapes. In non-neural cells, as in the brain, bioelectric signaling implements information processing, decision-making, and memory in regulating pattern and its remodeling. Thus, approaches used in computational neuroscience to understand goal-seeking neural systems offer a toolbox of techniques to model and control regenerative pattern formation. Here, we review recent data on developmental bioelectricity as a regulator of patterning, and propose that target morphology could be encoded within tissues as a kind of memory, using the same molecular mechanisms and algorithms so successfully exploited by the brain. We highlight the next steps of an unconventional research program, which may allow top-down control of growth and form for numerous applications in regenerative medicine and synthetic bioengineering.
Evidence of a molecular boundary lubricant at snakeskin surfaces

PubMed Central

Spinner, Marlene; Jaye, Cherno; Fischer, Daniel A.; Gorb, Stanislav N.; Weidner, Tobias

2015-01-01

During slithering locomotion the ventral scales at a snake's belly are in direct mechanical interaction with the environment, while the dorsal scales provide optical camouflage and thermoregulation. Recent work has demonstrated that compared to dorsal scales, ventral scales provide improved lubrication and wear protection. While biomechanic adaption of snake motion is of growing interest in the fields of material science and robotics, the mechanism for how ventral scales influence the friction between the snake and substrate, at the molecular level, is unknown. In this study, we characterize the outermost surface of snake scales using sum frequency generation (SFG) spectra and near-edge X-ray absorption fine structure (NEXAFS) images collected from recently shed California kingsnake (Lampropeltis californiae) epidermis. SFG's nonlinear optical selection rules provide information about the outermost surface of materials; NEXAFS takes advantage of the shallow escape depth of the electrons to probe the molecular structure of surfaces. Our analysis of the data revealed the existence of a previously unknown lipid coating on both the ventral and dorsal scales. Additionally, the molecular structure of this lipid coating closely aligns to the biological function: lipids on ventral scales form a highly ordered layer which provides both lubrication and wear protection at the snake's ventral surface. PMID:26655468
Evidence of a molecular boundary lubricant at snakeskin surfaces.

PubMed

Baio, Joe E; Spinner, Marlene; Jaye, Cherno; Fischer, Daniel A; Gorb, Stanislav N; Weidner, Tobias

2015-12-06

During slithering locomotion the ventral scales at a snake's belly are in direct mechanical interaction with the environment, while the dorsal scales provide optical camouflage and thermoregulation. Recent work has demonstrated that compared to dorsal scales, ventral scales provide improved lubrication and wear protection. While biomechanic adaption of snake motion is of growing interest in the fields of material science and robotics, the mechanism for how ventral scales influence the friction between the snake and substrate, at the molecular level, is unknown. In this study, we characterize the outermost surface of snake scales using sum frequency generation (SFG) spectra and near-edge X-ray absorption fine structure (NEXAFS) images collected from recently shed California kingsnake (Lampropeltis californiae) epidermis. SFG's nonlinear optical selection rules provide information about the outermost surface of materials; NEXAFS takes advantage of the shallow escape depth of the electrons to probe the molecular structure of surfaces. Our analysis of the data revealed the existence of a previously unknown lipid coating on both the ventral and dorsal scales. Additionally, the molecular structure of this lipid coating closely aligns to the biological function: lipids on ventral scales form a highly ordered layer which provides both lubrication and wear protection at the snake's ventral surface. © 2015 The Author(s).
Theoretical study of a molecular turbine.

PubMed

Perez-Carrasco, R; Sancho, J M

2013-10-01

We present an analytic and stochastic simulation study of a molecular engine working with a flux of particles as a turbine. We focus on the physical observables of velocity, flux, power, and efficiency. The control parameters are the external conservative force and the particle densities. We revise a simpler previous study by using a more realistic model containing multiple equidistant vanes complemented by stochastic simulations of the particles and the turbine. Here we show that the effect of the thermal fluctuations into the flux and the efficiency of these nanometric devices are relevant to the working scale of the system. The stochastic simulations of the Brownian motion of the particles and turbine support the simplified analytical calculations performed.
Bioluminescence in the Sea

NASA Astrophysics Data System (ADS)

Haddock, Steven H. D.; Moline, Mark A.; Case, James F.

2010-01-01

Bioluminescence spans all oceanic dimensions and has evolved many times—from bacteria to fish—to powerfully influence behavioral and ecosystem dynamics. New methods and technology have brought great advances in understanding of the molecular basis of bioluminescence, its physiological control, and its significance in marine communities. Novel tools derived from understanding the chemistry of natural light-producing molecules have led to countless valuable applications, culminating recently in a related Nobel Prize. Marine organisms utilize bioluminescence for vital functions ranging from defense to reproduction. To understand these interactions and the distributions of luminous organisms, new instruments and platforms allow observations on individual to oceanographic scales. This review explores recent advances, including the chemical and molecular, phylogenetic and functional, community and oceanographic aspects of bioluminescence.
Switchable host-guest systems on surfaces.

PubMed

Yang, Ying-Wei; Sun, Yu-Long; Song, Nan

2014-07-15

CONSPECTUS: For device miniaturization, nanotechnology follows either the "top-down" approach scaling down existing larger-scale devices or the "bottom-up' approach assembling the smallest possible building blocks to functional nanoscale entities. For synthetic nanodevices, self-assembly on surfaces is a superb method to achieve useful functions and enable their interactions with the surrounding world. Consequently, adaptability and responsiveness to external stimuli are other prerequisites for their successful operation. Mechanically interlocked molecules such as rotaxanes and catenanes, and their precursors, that is, molecular switches and supramolecular switches including pseudorotaxanes, are molecular machines or prototypes of machines capable of mechanical motion induced by chemical signals, biological inputs, light or redox processes as the external stimuli. Switching of these functional host-guest systems on surfaces becomes a fundamental requirement for artificial molecular machines to work, mimicking the molecular machines in nature, such as proteins and their assemblies operating at dynamic interfaces such as the surfaces of cell membranes. Current research endeavors in material science and technology are focused on developing either a new class of materials or materials with novel/multiple functionalities by shifting host-guest chemistry from solution phase to surfaces. In this Account, we present our most recent attempts of building monolayers of rotaxanes/pseudorotaxanes on surfaces, providing stimuli-induced macroscopic effects and further understanding on the switchable host-guest systems at interfaces. Biocompatible versions of molecular machines based on synthetic macrocycles, such as cucurbiturils, pillararenes, calixarenes, and cyclodextrins, have been employed to form self-assembled monolayers of gates on the surfaces of mesoporous silica nanoparticles to regulate the controlled release of cargo/drug molecules under a range of external stimuli, such as light, pH variations, competitive binding, and enzyme. Rotaxanes have also been assembled onto the surfaces of gold nanodisks and microcantilevers to realize active molecular plasmonics and synthetic molecular actuators for device fabrication and function. Pillararenes have been successfully used to control and aid the synthesis of gold nanoparticles, semiconducting quantum dots, and magnetic nanoparticles. The resulting organic-inorganic hydrid nanomaterials have been successfully used for controlled self-assembly, herbicide sensing and detection, pesticide removal, and so forth, taking advantage of the selective binding of pillarenes toward target molecules. Cyclodextrins have also been successfully functionalized onto the surface of gold nanoparticles to serve as recycling extractors for C60. Many interesting prototypes of nanodevices based on synthetic macrocycles and their host-guest chemistry have been constructed and served for different potential applications. This Account will be a summary of the efforts made mainly by us, and others, on the host-guest chemistry of synthetic macrocyclic compounds on the surfaces of different solid supports.
Self-Consistent Field Theories for the Role of Large Length-Scale Architecture in Polymers

NASA Astrophysics Data System (ADS)

Wu, David

At large length-scales, the architecture of polymers can be described by a coarse-grained specification of the distribution of branch points and monomer types within a molecule. This includes molecular topology (e.g., cyclic or branched) as well as distances between branch points or chain ends. Design of large length-scale molecular architecture is appealing because it offers a universal strategy, independent of monomer chemistry, to tune properties. Non-linear analogs of linear chains differ in molecular-scale properties, such as mobility, entanglements, and surface segregation in blends that are well-known to impact rheological, dynamical, thermodynamic and surface properties including adhesion and wetting. We have used Self-Consistent Field (SCF) theories to describe a number of phenomena associated with large length-scale polymer architecture. We have predicted the surface composition profiles of non-linear chains in blends with linear chains. These predictions are in good agreement with experimental results, including from neutron scattering, on a range of well-controlled branched (star, pom-pom and end-branched) and cyclic polymer architectures. Moreover, the theory allows explanation of the segregation and conformations of branched polymers in terms of effective surface potentials acting on the end and branch groups. However, for cyclic chains, which have no end or junction points, a qualitatively different topological mechanism based on conformational entropy drives cyclic chains to a surface, consistent with recent neutron reflectivity experiments. We have also used SCF theory to calculate intramolecular and intermolecular correlations for polymer chains in the bulk, dilute solution, and trapped at a liquid-liquid interface. Predictions of chain swelling in dilute star polymer solutions compare favorably with existing PRISM theory and swelling at an interface helps explain recent measurements of chain mobility at an oil-water interface. In collaboration with: Renfeng Hu, Colorado School of Mines, and Mark Foster, University of Akron. This work was supported by NSF Grants No. CBET- 0730692 and No. CBET-0731319.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lawrence R. Sita

Ferrocene-based molecular components for nanoelectronics offer a number of distinct advantages relative to all carbon frameworks due to metal-centered molecular states that should be closer in energy to the Fermi levels of the metal electrodes in metal / molecule / metal heterojunctions. Given this, the overall goal of the project was to investigate the conduction physics of a variety of proposed ferrocene diode / transistor designs in order to address the fundamental question; can electron transport within nm-length scale structures be modulated in a controlled fashion? During the funded period, substantial progress towards achieving this goal was made by surmountingmore » a number of scientific and technical obstacles. More specifically, a concise and general synthetic route to several mono- and diferrocene dithiols and monothiols was achieved that now allows for the directed and controlled assembly of a variety of metal / molecule /metal test structures for the single molecule conductance measurements and the fabrication of self-assembled monolayers (SAMs) on Au(111) that are amenable to quantitative electrochemical characterization of electron-transfer rates. Most importantly, by using an electromigrated test structure, reproducible I/V data for one of the ferrocene dithiol molecules have been collected which exhibit surprisingly high conductance. Exceptional agreement of this result with theory serves to substantiate the original hypothesis that metal-centered states within a molecular bridge can indeed serve to establish higher conductance relative to all-organic molecular bridges. Overall, the successful demonstration of the ability of ferrocene-molecular frameworks to serve as exceptional molecular conductors will play an important role in the continued evolution in design of molecular components for nanoelectronic devices, which in turn, will have a positive impact on the science and potential technologies associated with these systems.« less
Scales of Star Formation: Does Local Environment Matter?

NASA Astrophysics Data System (ADS)

Bittle, Lauren

2018-01-01

I will present my work on measuring molecular gas properties in local universe galaxies to assess the impact of local environment on the gas and thus star formation. I will also discuss the gas properties on spatial scales that span an order of magnitude to best understand the layers of star formation processes. Local environments within these galaxies include external mechanisms from starburst supernova shells, spiral arm structure, and superstar cluster radiation. Observations of CO giant molecular clouds (GMC) of ~150pc resolution in IC 10, the Local Group dwarf starburst, probe the large-scale diffuse gas, some of which are near supernova bubble ridges. We mapped CO clouds across the spiral NGC 7793 at intermediate scales of ~20pc resolution with ALMA. With the clouds, we can test theories of cloud formation and destruction in relation to the spiral arm pattern and cluster population from the HST LEGUS analysis. Addressing the smallest scales, I will show results of 30 Doradus ALMA observations of sub-parsec dense molecular gas clumps only 15pc away from a superstar cluster R136. Though star formation occurs directly from the collapse of densest molecular gas, we test theories of scale-free star formation, which suggests a constant slope of the mass function from ~150pc GMCs to sub-parsec clumps. Probing environments including starburst supernova shells, spiral arm structure, and superstar cluster radiation shed light on how these local external mechanisms affect the molecular gas at various scales of star formation.
Magnetic field generation by pointwise zero-helicity three-dimensional steady flow of an incompressible electrically conducting fluid

NASA Astrophysics Data System (ADS)

Rasskazov, Andrey; Chertovskih, Roman; Zheligovsky, Vladislav

2018-04-01

We introduce six families of three-dimensional space-periodic steady solenoidal flows, whose kinetic helicity density is zero at any point. Four families are analytically defined. Flows in four families have zero helicity spectrum. Sample flows from five families are used to demonstrate numerically that neither zero kinetic helicity density nor zero helicity spectrum prohibit generation of large-scale magnetic field by the two most prominent dynamo mechanisms: the magnetic α -effect and negative eddy diffusivity. Our computations also attest that such flows often generate small-scale field for sufficiently small magnetic molecular diffusivity. These findings indicate that kinetic helicity and helicity spectrum are not the quantities controlling the dynamo properties of a flow regardless of whether scale separation is present or not.
Molecular Precision at Micrometer Length Scales: Hierarchical Assembly of DNA-Protein Nanostructures.

PubMed

Schiffels, Daniel; Szalai, Veronika A; Liddle, J Alexander

2017-07-25

Robust self-assembly across length scales is a ubiquitous feature of biological systems but remains challenging for synthetic structures. Taking a cue from biology-where disparate molecules work together to produce large, functional assemblies-we demonstrate how to engineer microscale structures with nanoscale features: Our self-assembly approach begins by using DNA polymerase to controllably create double-stranded DNA (dsDNA) sections on a single-stranded template. The single-stranded DNA (ssDNA) sections are then folded into a mechanically flexible skeleton by the origami method. This process simultaneously shapes the structure at the nanoscale and directs the large-scale geometry. The DNA skeleton guides the assembly of RecA protein filaments, which provides rigidity at the micrometer scale. We use our modular design strategy to assemble tetrahedral, rectangular, and linear shapes of defined dimensions. This method enables the robust construction of complex assemblies, greatly extending the range of DNA-based self-assembly methods.
Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli

PubMed Central

Gat-Viks, Irit; Chevrier, Nicolas; Wilentzik, Roni; Eisenhaure, Thomas; Raychowdhury, Raktima; Steuerman, Yael; Shalek, Alex; Hacohen, Nir; Amit, Ido; Regev, Aviv

2013-01-01

Individual genetic variation affects gene expression in response to stimuli, often by influencing complex molecular circuits. Here we combine genomic and intermediate-scale transcriptional profiling with computational methods to identify variants that affect the responsiveness of genes to stimuli (responsiveness QTLs; reQTLs) and to position these variants in molecular circuit diagrams. We apply this approach to study variation in transcriptional responsiveness to pathogen components in dendritic cells from recombinant inbred mouse strains. We identify reQTLs that correlate with particular stimuli and position them in known pathways. For example, in response to a virus-like stimulus, a trans-acting variant acts as an activator of the antiviral response; using RNAi, we identify Rgs16 as the likely causal gene. Our approach charts an experimental and analytic path to decipher the mechanisms underlying genetic variation in circuits that control responses to stimuli. PMID:23503680
Final Report: Molecular mechanisms and kinetics of microbial anaerobic nitrate-dependent U(IV) and Fe(II) oxidation

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Day, Peggy A.; Asta, Maria P.; Kanematsu, Masakazu

2015-02-27

In this project, we combined molecular genetic, spectroscopic, and microscopic techniques with kinetic and reactive transport studies to describe and quantify biotic and abiotic mechanisms underlying anaerobic, nitrate-dependent U(IV) and Fe(II) oxidation, which influences the long-term efficacy of in situ reductive immobilization of uranium at DOE sites. In these studies, Thiobacillus denitrificans, an autotrophic bacterium that catalyzes anaerobic U(IV) and Fe(II) oxidation, was used to examine coupled oxidation-reduction processes under either biotic (enzymatic) or abiotic conditions in batch and column experiments with biogenically produced UIVO2(s). Synthesis and quantitative analysis of coupled chemical and transport processes were done with the reactivemore » transport modeling code Crunchflow. Research focused on identifying the primary redox proteins that catalyze metal oxidation, environmental factors that influence protein expression, and molecular-scale geochemical factors that control the rates of biotic and abiotic oxidation.« less
Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli.

PubMed

Gat-Viks, Irit; Chevrier, Nicolas; Wilentzik, Roni; Eisenhaure, Thomas; Raychowdhury, Raktima; Steuerman, Yael; Shalek, Alex K; Hacohen, Nir; Amit, Ido; Regev, Aviv

2013-04-01

Individual genetic variation affects gene responsiveness to stimuli, often by influencing complex molecular circuits. Here we combine genomic and intermediate-scale transcriptional profiling with computational methods to identify variants that affect the responsiveness of genes to stimuli (responsiveness quantitative trait loci or reQTLs) and to position these variants in molecular circuit diagrams. We apply this approach to study variation in transcriptional responsiveness to pathogen components in dendritic cells from recombinant inbred mouse strains. We identify reQTLs that correlate with particular stimuli and position them in known pathways. For example, in response to a virus-like stimulus, a trans-acting variant responds as an activator of the antiviral response; using RNA interference, we identify Rgs16 as the likely causal gene. Our approach charts an experimental and analytic path to decipher the mechanisms underlying genetic variation in circuits that control responses to stimuli.
Inter-Fullerene Electronic Coupling Controls the Efficiency of Photoinduced Charge Generation in Organic Bulk Heterojunctions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larson, Bryon W.; Reid, Obadiah G.; Coffey, David C.

2016-09-26

Photoinduced charge generation (PCG) dynamics are notoriously difficult to correlate with specific molecular properties in device relevant polymer:fullerene organic photovoltaic blend films due to the highly complex nature of the solid state blend morphology. Here, this study uses six judiciously selected trifluoromethylfullerenes blended with the prototypical polymer poly(3-hexylthiophene) and measure the PCG dynamics in 50 fs-500 ns time scales with time-resolved microwave conductivity and femtosecond transient absorption spectroscopy. The isomeric purity and thorough chemical characterization of the fullerenes used in this study allow for a detailed correlation between molecular properties, driving force, local intermolecular electronic coupling and, ultimately, the efficiencymore » of PCG yield. The findings show that the molecular design of the fullerene not only determines inter-fullerene electronic coupling, but also influences the decay dynamics of free holes in the donor phase even when the polymer microstructure remains unchanged.« less
Crankshafts: using simple, flat C2h-symmetric molecules to direct the assembly of chiral 2D nanopatterns.

PubMed

Zhou, Hui; Wuest, James D

2013-06-18

Linear D2h-symmetric bisisophthalic acids 1 and 2 and related substances have well-defined flattened structures, high affinities for graphite, and strong abilities to engage in specific intermolecular interactions. Their adsorption produces characteristic nanopatterns that reveal how 2D molecular organization can be controlled by reliable interadsorbate interactions such as hydrogen bonds when properly oriented by molecular geometry. In addition, the behavior of these compounds shows how large-scale organization can be obstructed by programming molecules to associate strongly according to competing motifs that have similar stability and can coexist smoothly without creating significant defects. Analogous new bisisophthalic acids 3a and 4a have similar associative properties, and their unique C2h-symmetric crankshaft geometry gives them the added ability to probe the poorly understood effect of chirality on molecular organization. Their adsorption shows how nanopatterns composed predictably of a single enantiomer can be obtained by depositing molecules that can respect established rules of association only by accepting neighbors of the same configuration. In addition, an analysis of the adsorption of crankshaft compounds 3a and 4a and their derivatives by STM reveals directly on the molecular level how kinetics and thermodynamics compete to control the crystallization of chiral compounds. In such ways, detailed studies of the adsorption of properly designed compounds on surfaces are proving to be a powerful way to discover and test rules that broadly govern molecular organization in both 2D and 3D.
Top-down models in biology: explanation and control of complex living systems above the molecular level.

PubMed

Pezzulo, Giovanni; Levin, Michael

2016-11-01

It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering. © 2016 The Author(s).
Top-down models in biology: explanation and control of complex living systems above the molecular level

PubMed Central

2016-01-01

It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering. PMID:27807271
Implementation of Shifted Periodic Boundary Conditions in the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Software

DTIC Science & Technology

2015-08-01

Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) Software by N Scott Weingarten and James P Larentzos Approved for...Massively Parallel Simulator ( LAMMPS ) Software by N Scott Weingarten Weapons and Materials Research Directorate, ARL James P Larentzos Engility...Shifted Periodic Boundary Conditions in the Large-Scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) Software 5a. CONTRACT NUMBER 5b
Molecular environmental geochemistry

NASA Astrophysics Data System (ADS)

O'Day, Peggy A.

1999-05-01

The chemistry, mobility, and bioavailability of contaminant species in the natural environment are controlled by reactions that occur in and among solid, aqueous, and gas phases. These reactions are varied and complex, involving changes in chemical form and mass transfer among inorganic, organic, and biochemical species. The field of molecular environmental geochemistry seeks to apply spectroscopic and microscopic probes to the mechanistic understanding of environmentally relevant chemical processes, particularly those involving contaminants and Earth materials. In general, empirical geochemical models have been shown to lack uniqueness and adequate predictive capability, even in relatively simple systems. Molecular geochemical tools, when coupled with macroscopic measurements, can provide the level of chemical detail required for the credible extrapolation of contaminant reactivity and bioavailability over ranges of temperature, pressure, and composition. This review focuses on recent advances in the understanding of molecular chemistry and reaction mechanisms at mineral surfaces and mineral-fluid interfaces spurred by the application of new spectroscopies and microscopies. These methods, such as synchrotron X-ray absorption and scattering techniques, vibrational and resonance spectroscopies, and scanning probe microscopies, provide direct chemical information that can elucidate molecular mechanisms, including element speciation, ligand coordination and oxidation state, structural arrangement and crystallinity on different scales, and physical morphology and topography of surfaces. Nonvacuum techniques that allow examination of reactions in situ (i.e., with water or fluids present) and in real time provide direct links between molecular structure and reactivity and measurements of kinetic rates or thermodynamic properties. Applications of these diverse probes to laboratory model systems have provided fundamental insight into inorganic and organic reactions at mineral surfaces and mineral-water interfaces. A review of recent studies employing molecular characterizations of soils, sediments, and biological samples from contaminated sites exemplifies the utility and benefits, as well as the challenge, of applying molecular probes to complicated natural materials. New techniques, technological advances, and the crossover of methods from other disciplines such as biochemistry and materials science promise better examination of environmental chemical processes in real time and at higher resolution, and will further the integration of molecular information into field-scale chemical and hydrologic models.
Combinatorial screening of halide perovskite thin films and solar cells by mask-defined IR laser molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Kawashima, Kazuhiro; Okamoto, Yuji; Annayev, Orazmuhammet; Toyokura, Nobuo; Takahashi, Ryota; Lippmaa, Mikk; Itaka, Kenji; Suzuki, Yoshikazu; Matsuki, Nobuyuki; Koinuma, Hideomi

2017-12-01

As an extension of combinatorial molecular layer epitaxy via ablation of perovskite oxides by a pulsed excimer laser, we have developed a laser molecular beam epitaxy (MBE) system for parallel integration of nano-scaled thin films of organic-inorganic hybrid materials. A pulsed infrared (IR) semiconductor laser was adopted for thermal evaporation of organic halide (A-site: CH3NH3I) and inorganic halide (B-site: PbI2) powder targets to deposit repeated A/B bilayer films where the thickness of each layer was controlled on molecular layer scale by programming the evaporation IR laser pulse number, length, or power. The layer thickness was monitored with an in situ quartz crystal microbalance and calibrated against ex situ stylus profilometer measurements. A computer-controlled movable mask system enabled the deposition of combinatorial thin film libraries, where each library contains a vertically homogeneous film with spatially programmable A- and B-layer thicknesses. On the composition gradient film, a hole transport Spiro-OMeTAD layer was spin-coated and dried followed by the vacuum evaporation of Ag electrodes to form the solar cell. The preliminary cell performance was evaluated by measuring I-V characteristics at seven different positions on the 12.5 mm × 12.5 mm combinatorial library sample with seven 2 mm × 4 mm slits under a solar simulator irradiation. The combinatorial solar cell library clearly demonstrated that the energy conversion efficiency sharply changes from nearly zero to 10.2% as a function of the illumination area in the library. The exploration of deposition parameters for obtaining optimum performance could thus be greatly accelerated. Since the thickness ratio of PbI2 and CH3NH3I can be freely chosen along the shadow mask movement, these experiments show the potential of this system for high-throughput screening of optimum chemical composition in the binary film library and application to halide perovskite solar cell.
Combinatorial screening of halide perovskite thin films and solar cells by mask-defined IR laser molecular beam epitaxy.

PubMed

Kawashima, Kazuhiro; Okamoto, Yuji; Annayev, Orazmuhammet; Toyokura, Nobuo; Takahashi, Ryota; Lippmaa, Mikk; Itaka, Kenji; Suzuki, Yoshikazu; Matsuki, Nobuyuki; Koinuma, Hideomi

2017-01-01

As an extension of combinatorial molecular layer epitaxy via ablation of perovskite oxides by a pulsed excimer laser, we have developed a laser molecular beam epitaxy (MBE) system for parallel integration of nano-scaled thin films of organic-inorganic hybrid materials. A pulsed infrared (IR) semiconductor laser was adopted for thermal evaporation of organic halide (A-site: CH 3 NH 3 I) and inorganic halide (B-site: PbI 2 ) powder targets to deposit repeated A/B bilayer films where the thickness of each layer was controlled on molecular layer scale by programming the evaporation IR laser pulse number, length, or power. The layer thickness was monitored with an in situ quartz crystal microbalance and calibrated against ex situ stylus profilometer measurements. A computer-controlled movable mask system enabled the deposition of combinatorial thin film libraries, where each library contains a vertically homogeneous film with spatially programmable A- and B-layer thicknesses. On the composition gradient film, a hole transport Spiro-OMeTAD layer was spin-coated and dried followed by the vacuum evaporation of Ag electrodes to form the solar cell. The preliminary cell performance was evaluated by measuring I - V characteristics at seven different positions on the 12.5 mm × 12.5 mm combinatorial library sample with seven 2 mm × 4 mm slits under a solar simulator irradiation. The combinatorial solar cell library clearly demonstrated that the energy conversion efficiency sharply changes from nearly zero to 10.2% as a function of the illumination area in the library. The exploration of deposition parameters for obtaining optimum performance could thus be greatly accelerated. Since the thickness ratio of PbI 2 and CH 3 NH 3 I can be freely chosen along the shadow mask movement, these experiments show the potential of this system for high-throughput screening of optimum chemical composition in the binary film library and application to halide perovskite solar cell.
The role of hydrology in annual organic carbon loads and terrestrial organic matter export from a midwestern agricultural watershed

NASA Astrophysics Data System (ADS)

Dalzell, Brent J.; Filley, Timothy R.; Harbor, Jon M.

2007-03-01

Defining the control that hydrology exerts on organic carbon (OC) export at the watershed scale is important for understanding how the source and quantity of OC in streams and rivers is influenced by climate change or by landscape drainage. To this end, molecular (lignin phenol), stable carbon isotope, and dissolved organic carbon (DOC) data were collected over a range of flow conditions to examine the influence of hydrology on annual OC export from an 850 km 2 Midwestern United States agricultural watershed located in west central Indiana. In years 2002 and 2003, modeled annual DOC loads were 19.5 and 14.1 kg ha -1yr -1, while 71% and 85%, respectively, of the total annual OC was exported in flow events occurring during less than 20% of that time. These results highlight the importance of short-duration, high-discharge events (common in smaller watersheds) in controlling annual OC export. Based on reported increases in annual stream discharge coupled with current estimates of DOC export, annual DOC loads in this watershed may have increased by up to 40% over the past 50 years. Molecular (lignin phenol) characterization of quantity and relative degradation state of terrestrial OC shows as much temporal variability of lignin parameters (in high molecular weight dissolved organic carbon) in this one watershed as that demonstrated in previously published studies of dissolved organic matter in the Mississippi and Amazon Rivers. These results suggest that hydrologic variability is at least as important in determining the nature and extent of OC export as geographic variability. Moreover, molecular and bulk stable carbon isotope data from high molecular weight dissolved organic carbon and colloidal organic carbon showed that increased stream flow from the study watershed was responsible for increased export of agriculturally derived OC. When considered in the context of results from other studies that show the importance of flood events and in-stream processing of terrestrial organic carbon, our results show how hydrologic variability in smaller watersheds can reflect landscape-scale carbon dynamics in ways that cannot necessarily be measured at the outlets of large rivers due to multiple source signals and attenuated hydrology.
Thermodynamic scaling of dynamic properties of liquid crystals: Verifying the scaling parameters using a molecular model

NASA Astrophysics Data System (ADS)

Satoh, Katsuhiko

2013-08-01

The thermodynamic scaling of molecular dynamic properties of rotation and thermodynamic parameters in a nematic phase was investigated by a molecular dynamic simulation using the Gay-Berne potential. A master curve for the relaxation time of flip-flop motion was obtained using thermodynamic scaling, and the dynamic property could be solely expressed as a function of TV^{γ _τ }, where T and V are the temperature and volume, respectively. The scaling parameter γτ was in excellent agreement with the thermodynamic parameter Γ, which is the logarithm of the slope of a line plotted for the temperature and volume at constant P2. This line was fairly linear, and as good as the line for p-azoxyanisole or using the highly ordered small cluster model. The equivalence relation between Γ and γτ was compared with results obtained from the highly ordered small cluster model. The possibility of adapting the molecular model for the thermodynamic scaling of other dynamic rotational properties was also explored. The rotational diffusion constant and rotational viscosity coefficients, which were calculated using established theoretical and experimental expressions, were rescaled onto master curves with the same scaling parameters. The simulation illustrates the universal nature of the equivalence relation for liquid crystals.
Motion of Fullerenes around Topological Defects on Metals: Implications for the Progress of Molecular Scale Devices.

PubMed

Nirmalraj, Peter; Daly, Ronan; Martin, Nazario; Thompson, Damien

2017-03-08

Research on motion of molecules in the presence of thermal noise is central for progress in two-terminal molecular scale electronic devices. However, it is still unclear what influence imperfections in bottom metal electrode surface can have on molecular motion. Here, we report a two-layer crowding study, detailing the early stages of surface motion of fullerene molecules on Au(111) with nanoscale pores in a n-tetradecane chemical environment. The motion of the fullerenes is directed by crowding of the underlying n-tetradecane molecules around the pore fringes at the liquid-solid interface. We observe in real-space the growth of molecular populations around different pore geometries. Supported by atomic-scale modeling, our findings extend the established picture of molecular crowding by revealing that trapped solvent molecules serve as prime nucleation sites at nanopore fringes.
Chemomechanics with Molecular Force Probes

DTIC Science & Technology

2010-03-30

at scales >50 nm) [ 1 –5]. Such coupling affects the rate at which the chemical reaction occurs and therefore must be accounted for in any kinetic...reporting burden for the collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching...it does not display a currently valid OMB control number. 1 . REPORT DATE 2010 2. REPORT TYPE 3. DATES COVERED 00-00-2010 to 00-00-2010 4
Embedded Clusters

NASA Astrophysics Data System (ADS)

Ascenso, Joana

The past decade has seen an increase of star formation studies made at the molecular cloud scale, motivated mostly by the deployment of a wealth of sensitive infrared telescopes and instruments. Embedded clusters, long recognised as the basic units of coherent star formation in molecular clouds, are now seen to inhabit preferentially cluster complexes tens of parsecs across. This chapter gives an overview of some important properties of the embedded clusters in these complexes and of the complexes themselves, along with the implications of viewing star formation as a molecular-cloud scale process rather than an isolated process at the scale of clusters.

Cellular automata with object-oriented features for parallel molecular network modeling.

PubMed

Zhu, Hao; Wu, Yinghui; Huang, Sui; Sun, Yan; Dhar, Pawan

2005-06-01

Cellular automata are an important modeling paradigm for studying the dynamics of large, parallel systems composed of multiple, interacting components. However, to model biological systems, cellular automata need to be extended beyond the large-scale parallelism and intensive communication in order to capture two fundamental properties characteristic of complex biological systems: hierarchy and heterogeneity. This paper proposes extensions to a cellular automata language, Cellang, to meet this purpose. The extended language, with object-oriented features, can be used to describe the structure and activity of parallel molecular networks within cells. Capabilities of this new programming language include object structure to define molecular programs within a cell, floating-point data type and mathematical functions to perform quantitative computation, message passing capability to describe molecular interactions, as well as new operators, statements, and built-in functions. We discuss relevant programming issues of these features, including the object-oriented description of molecular interactions with molecule encapsulation, message passing, and the description of heterogeneity and anisotropy at the cell and molecule levels. By enabling the integration of modeling at the molecular level with system behavior at cell, tissue, organ, or even organism levels, the program will help improve our understanding of how complex and dynamic biological activities are generated and controlled by parallel functioning of molecular networks. Index Terms-Cellular automata, modeling, molecular network, object-oriented.
The Conductance of Porphyrin-Based Molecular Nanowires Increases with Length.

PubMed

Algethami, Norah; Sadeghi, Hatef; Sangtarash, Sara; Lambert, Colin J

2018-06-13

High electrical conductance molecular nanowires are highly desirable components for future molecular-scale circuitry, but typically molecular wires act as tunnel barriers and their conductance decays exponentially with length. Here, we demonstrate that the conductance of fused-oligo-porphyrin nanowires can be either length independent or increase with length at room temperature. We show that this negative attenuation is an intrinsic property of fused-oligo-porphyrin nanowires, but its manifestation depends on the electrode material or anchor groups. This highly desirable, nonclassical behavior signals the quantum nature of transport through such wires. It arises because with increasing length the tendency for electrical conductance to decay is compensated by a decrease in their highest occupied molecular orbital-lowest unoccupied molecular orbital gap. Our study reveals the potential of these molecular wires as interconnects in future molecular-scale circuitry.
Automatic Molecular Design using Evolutionary Techniques

NASA Technical Reports Server (NTRS)

Globus, Al; Lawton, John; Wipke, Todd; Saini, Subhash (Technical Monitor)

1998-01-01

Molecular nanotechnology is the precise, three-dimensional control of materials and devices at the atomic scale. An important part of nanotechnology is the design of molecules for specific purposes. This paper describes early results using genetic software techniques to automatically design molecules under the control of a fitness function. The fitness function must be capable of determining which of two arbitrary molecules is better for a specific task. The software begins by generating a population of random molecules. The population is then evolved towards greater fitness by randomly combining parts of the better individuals to create new molecules. These new molecules then replace some of the worst molecules in the population. The unique aspect of our approach is that we apply genetic crossover to molecules represented by graphs, i.e., sets of atoms and the bonds that connect them. We present evidence suggesting that crossover alone, operating on graphs, can evolve any possible molecule given an appropriate fitness function and a population containing both rings and chains. Prior work evolved strings or trees that were subsequently processed to generate molecular graphs. In principle, genetic graph software should be able to evolve other graph representable systems such as circuits, transportation networks, metabolic pathways, computer networks, etc.
Confinement and controlling the effective compressive stiffness of carbyne

NASA Astrophysics Data System (ADS)

Kocsis, Ashley J.; Aditya Reddy Yedama, Neta; Cranford, Steven W.

2014-08-01

Carbyne is a one-dimensional chain of carbon atoms, consisting of repeating sp-hybridized groups, thereby representing a minimalist molecular rod or chain. While exhibiting exemplary mechanical properties in tension (a 1D modulus on the order of 313 nN and a strength on the order of 11 nN), its use as a structural component at the molecular scale is limited due to its relative weakness in compression and the immediate onset of buckling under load. To circumvent this effect, here, we probe the effect of confinement to enhance the mechanical behavior of carbyne chains in compression. Through full atomistic molecular dynamics, we characterize the mechanical properties of a free (unconfined chain) and explore the effect of confinement radius (R), free chain length (L) and temperature (T) on the effective compressive stiffness of carbyne chains and demonstrate that the stiffness can be tuned over an order of magnitude (from approximately 0.54 kcal mol-1 Å2 to 46 kcal mol-1 Å2) by geometric control. Confinement may inherently stabilize the chains, potentially providing a platform for the synthesis of extraordinarily long chains (tens of nanometers) with variable compressive response.
Recent transmission of Mycobacterium tuberculosis in China: the implication of molecular epidemiology for tuberculosis control.

PubMed

Yang, Chongguang; Gao, Qian

2018-02-01

Tuberculosis (TB) has remained an ongoing concern in China. The national scale-up of the Directly Observed Treatment, Short Course (DOTS) program has accelerated the fight against TB in China. Nevertheless, many challenges still remain, including the spread of drug-resistant strains, high disease burden in rural areas, and enormous rural-to-urban migrations. Whether incident active TB represents recent transmission or endogenous reactivation has helped to prioritize the strategies for TB control. Evidence from molecular epidemiology studies has delineated the recent transmission of Mycobacterium tuberculosis (M. tuberculosis) strains in many settings. However, the transmission patterns of TB in most areas of China are still not clear. Studies carried out to date could not capture the real burden of recent transmission of the disease in China because of the retrospective study design, incomplete sampling, and use of low-resolution genotyping methods. We reviewed the implementations of molecular epidemiology of TB in China, the estimated disease burden due to recent transmission of M. tuberculosis strains, the primary transmission of drug-resistant TB, and the evaluation of a feasible genotyping method of M. tuberculosis strains in circulation.
Sub-grid-scale description of turbulent magnetic reconnection in magnetohydrodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Widmer, F., E-mail: widmer@mps.mpg.de; Institut für Astrophysik, Georg-August-Universität, Friedrich-Hund-Platz 1, 37077 Göttingen; Büchner, J.

Magnetic reconnection requires, at least locally, a non-ideal plasma response. In collisionless space and astrophysical plasmas, turbulence could transport energy from large to small scales where binary particle collisions are rare. We have investigated the influence of small scale magnetohydrodynamics (MHD) turbulence on the reconnection rate in the framework of a compressible MHD approach including sub-grid-scale (SGS) turbulence. For this sake, we considered Harris-type and force-free current sheets with finite guide magnetic fields directed out of the reconnection plane. The goal is to find out whether unresolved by conventional simulations MHD turbulence can enhance the reconnection process in high-Reynolds-number astrophysicalmore » plasmas. Together with the MHD equations, we solve evolution equations for the SGS energy and cross-helicity due to turbulence according to a Reynolds-averaged turbulence model. The SGS turbulence is self-generated and -sustained through the inhomogeneities of the mean fields. By this way, the feedback of the unresolved turbulence into the MHD reconnection process is taken into account. It is shown that the turbulence controls the regimes of reconnection by its characteristic timescale τ{sub t}. The dependence on resistivity was investigated for large-Reynolds-number plasmas for Harris-type as well as force-free current sheets with guide field. We found that magnetic reconnection depends on the relation between the molecular and apparent effective turbulent resistivity. We found that the turbulence timescale τ{sub t} decides whether fast reconnection takes place or whether the stored energy is just diffused away to small scale turbulence. If the amount of energy transferred from large to small scales is enhanced, fast reconnection can take place. Energy spectra allowed us to characterize the different regimes of reconnection. It was found that reconnection is even faster for larger Reynolds numbers controlled by the molecular resistivity η, as long as the initial level of turbulence is not too large. This implies that turbulence plays an important role to reach the limit of fast reconnection in large Reynolds number plasmas even for smaller amounts of turbulence.« less
Controllable Synthesis and Catalytic Performance of Nanocrystals of Rare-Earth-Polyoxometalates.

PubMed

Li, Shujun; Zhou, Yanfang; Peng, Qingpo; Wang, Ruoya; Feng, Xiaoge; Liu, Shuxia; Ma, Xiaoming; Ma, Nana; Zhang, Jie; Chang, Yi; Zheng, Zhiping; Chen, Xuenian

2018-06-04

Large-scale isolation of nanocrystals of rare-earth-polyoxometalates (RE-POMs) catalysts is important in fundamental research and applications. Here, we synthesized a family of monomeric RE-POMs by the self-assembly of Ta/W mixed-addendum POM {P 2 W 15 Ta 3 O 62 } and rare-earth (RE) ions. These RE-POMs with molecular formulas of [RE(H 2 O) 7 ] 3 P 2 W 15 Ta 3 O 62 · nH 2 O (RE = Y, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu) are all electroneutral molecular clusters, insoluble in water and common organic solvents. The electronic structures, electrochemical properties, and catalytic activities of them have been investigated by experimental and computational methods. In particular, based on a mild and controllable synthetic process, a convenient and controllable approach to prepare nanocrystals and self-organized aggregates of these monomers has been developed. They exhibit remarkable heterogeneous catalytic activity for cyanosilylation. Both the increased Lewis acid strength of RE in the title compounds, as indicated by theoretical calculations, and the decreased particle size contribute to their high catalytic performances.
Bose-Einstein Condensates in 1D Optical Lattices: Nonlinearity and Wannier-Stark Spectra

NASA Astrophysics Data System (ADS)

Arimondo, Ennio; Ciampini, Donatella; Morsch, Oliver

The development of powerful laser cooling and trapping techniques has made possible the controlled realization of dense and cold gaseous samples, thus opening the way for investigations in the ultracold temperature regimes not accessible with conventional techniques. A Bose-Einstein condensate (BEC) represents a peculiar gaseous state where all the particles reside in the same quantum mechanical state. Therefore BECs exhibit quantum mechanical phe-nomena on a macroscopic scale with a single quantum mechanical wavefunction describing the external degrees of freedom. That control of the external degrees of freedom is combined with a precise control of the internal degrees. The BEC investigation has become a very active area of research in contem-porary physics. The BEC study encompasses different subfields of physics, i.e., atomic and molecular physics, quantum optics, laser spectroscopy, solid state physics. Atomic physics and laser spectroscopy provide the methods for creating and manipulating the atomic and molecular BECs. However owing to the interactions between the particles composing the condensate and to the configuration of the external potential, concepts and methods from solid state physics are extensively used for BEC description.
Characterization of chitin extracted from fish scales of marine fish species purchased from local markets in North Sulawesi, Indonesia

NASA Astrophysics Data System (ADS)

Rumengan, I. F. M.; Suptijah, P.; Wullur, S.; Talumepa, A.

2017-10-01

Chitin is a biodegradable biopolymer with a variety of commercial applications, including in the food food-supplement industries as a marine-derived nutraceutical. The purpose of this study was to characterize the molecular structure of chitin extracted from fish scales of important marine fish purchased from local markets in North Sulawesi. Chitin compound material was obtained from a specific fish scale, and then sequentially carrying out a boiling treatment to separate it from a complex with collagen. From the scales of two fish species, parrotfish (Chlorurus sordidus) and red snapper (Lutjanus argentimaculatus), the rendemen of chitin obtained were 45 % and 33%, respectively. Structural characteristics of the chitin were discussed by FTIR (Fourier Transform Infrared) analysis data. FTIR analysis was done using infrared spectroscopy, which is the resulting spectrum represents the molecular absorption and transmission, creating a molecular fingerprint of the sample. The molecular structure of chitin, C18H26N2O10, where the hydroxyl group on the second carbon replaced by acetyl amide, was shown by the infrared spectra. In the infrared spectra, chitin from parrot fish scales indicated the amide band at 1627.13 cm-1, and chitin from red snapper fish scales the amide band at 1648.09 cm-1 which are a typical one for marine chitin. The hydroxyl and amino bands at the ranged spectra up to 3500 cm-1. The yields of chitin isolated from fish scale were relatively huge. Some treatments are necessary to confirm the molecular conformation and deacetylation behavior. All products from the extraction of fish scales could be more accessible for structural modifications to develop biocompatible materials for pharmaceutical purposes.
Engineering the thermal conductivity along an individual silicon nanowire by selective helium ion irradiation.

PubMed

Zhao, Yunshan; Liu, Dan; Chen, Jie; Zhu, Liyan; Belianinov, Alex; Ovchinnikova, Olga S; Unocic, Raymond R; Burch, Matthew J; Kim, Songkil; Hao, Hanfang; Pickard, Daniel S; Li, Baowen; Thong, John T L

2017-06-27

The ability to engineer the thermal conductivity of materials allows us to control the flow of heat and derive novel functionalities such as thermal rectification, thermal switching and thermal cloaking. While this could be achieved by making use of composites and metamaterials at bulk length-scales, engineering the thermal conductivity at micro- and nano-scale dimensions is considerably more challenging. In this work, we show that the local thermal conductivity along a single Si nanowire can be tuned to a desired value (between crystalline and amorphous limits) with high spatial resolution through selective helium ion irradiation with a well-controlled dose. The underlying mechanism is understood through molecular dynamics simulations and quantitative phonon-defect scattering rate analysis, where the behaviour of thermal conductivity with dose is attributed to the accumulation and agglomeration of scattering centres at lower doses. Beyond a threshold dose, a crystalline-amorphous transition was observed.
Engineering the thermal conductivity along an individual silicon nanowire by selective helium ion irradiation

PubMed Central

Zhao, Yunshan; Liu, Dan; Chen, Jie; Zhu, Liyan; Belianinov, Alex; Ovchinnikova, Olga S.; Unocic, Raymond R.; Burch, Matthew J.; Kim, Songkil; Hao, Hanfang; Pickard, Daniel S.; Li, Baowen; Thong, John T. L.

2017-01-01

The ability to engineer the thermal conductivity of materials allows us to control the flow of heat and derive novel functionalities such as thermal rectification, thermal switching and thermal cloaking. While this could be achieved by making use of composites and metamaterials at bulk length-scales, engineering the thermal conductivity at micro- and nano-scale dimensions is considerably more challenging. In this work, we show that the local thermal conductivity along a single Si nanowire can be tuned to a desired value (between crystalline and amorphous limits) with high spatial resolution through selective helium ion irradiation with a well-controlled dose. The underlying mechanism is understood through molecular dynamics simulations and quantitative phonon-defect scattering rate analysis, where the behaviour of thermal conductivity with dose is attributed to the accumulation and agglomeration of scattering centres at lower doses. Beyond a threshold dose, a crystalline-amorphous transition was observed. PMID:28653663
Engineering the thermal conductivity along an individual silicon nanowire by selective helium ion irradiation

DOE PAGES

Zhao, Yunshan; Liu, Dan; Chen, Jie; ...

2017-06-27

The ability to engineer the thermal conductivity of materials allows us to control the flow of heat and derive novel functionalities such as thermal rectification, thermal switching and thermal cloaking. While this could be achieved by making use of composites and metamaterials at bulk length-scales, engineering the thermal conductivity at micro- and nano-scale dimensions is considerably more challenging. Here, we show that the local thermal conductivity along a single Si nanowire can be tuned to a desired value (between crystalline and amorphous limits) with high spatial resolution through selective helium ion irradiation with a well-controlled dose. The underlying mechanism ismore » understood through molecular dynamics simulations and quantitative phonon-defect scattering rate analysis, where the behaviour of thermal conductivity with dose is attributed to the accumulation and agglomeration of scattering centres at lower doses. Finally, we observed threshold dose beyond a crystalline-amorphous transition.« less
Engineering the thermal conductivity along an individual silicon nanowire by selective helium ion irradiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Yunshan; Liu, Dan; Chen, Jie

The ability to engineer the thermal conductivity of materials allows us to control the flow of heat and derive novel functionalities such as thermal rectification, thermal switching and thermal cloaking. While this could be achieved by making use of composites and metamaterials at bulk length-scales, engineering the thermal conductivity at micro- and nano-scale dimensions is considerably more challenging. Here, we show that the local thermal conductivity along a single Si nanowire can be tuned to a desired value (between crystalline and amorphous limits) with high spatial resolution through selective helium ion irradiation with a well-controlled dose. The underlying mechanism ismore » understood through molecular dynamics simulations and quantitative phonon-defect scattering rate analysis, where the behaviour of thermal conductivity with dose is attributed to the accumulation and agglomeration of scattering centres at lower doses. Finally, we observed threshold dose beyond a crystalline-amorphous transition.« less
Molecular and nanoscale materials and devices in electronics.

PubMed

Fu, Lei; Cao, Lingchao; Liu, Yunqi; Zhu, Daoben

2004-12-13

Over the past several years, there have been many significant advances toward the realization of electronic computers integrated on the molecular scale and a much greater understanding of the types of materials that will be useful in molecular devices and their properties. It was demonstrated that individual molecules could serve as incomprehensibly tiny switch and wire one million times smaller than those on conventional silicon microchip. This has resulted very recently in the assembly and demonstration of tiny computer logic circuits built from such molecular scale devices. The purpose of this review is to provide a general introduction to molecular and nanoscale materials and devices in electronics.
Exploring the Ability of a Coarse-grained Potential to Describe the Stress-strain Response of Glassy Polystyrene

DTIC Science & Technology

2012-10-01

using the open-source code Large-scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) (http://lammps.sandia.gov) (23). The commercial...parameters are proprietary and cannot be ported to the LAMMPS 4 simulation code. In our molecular dynamics simulations at the atomistic resolution, we...IBI iterative Boltzmann inversion LAMMPS Large-scale Atomic/Molecular Massively Parallel Simulator MAPS Materials Processes and Simulations MS
Molecular deformation mechanisms of the wood cell wall material.

PubMed

Jin, Kai; Qin, Zhao; Buehler, Markus J

2015-02-01

Wood is a biological material with outstanding mechanical properties resulting from its hierarchical structure across different scales. Although earlier work has shown that the cellular structure of wood is a key factor that renders it excellent mechanical properties at light weight, the mechanical properties of the wood cell wall material itself still needs to be understood comprehensively. The wood cell wall material features a fiber reinforced composite structure, where cellulose fibrils act as stiff fibers, and hemicellulose and lignin molecules act as soft matrix. The angle between the fiber direction and the loading direction has been found to be the key factor controlling the mechanical properties. However, how the interactions between theses constitutive molecules contribute to the overall properties is still unclear, although the shearing between fibers has been proposed as a primary deformation mechanism. Here we report a molecular model of the wood cell wall material with atomistic resolution, used to assess the mechanical behavior under shear loading in order to understand the deformation mechanisms at the molecular level. The model includes an explicit description of cellulose crystals, hemicellulose, as well as lignin molecules arranged in a layered nanocomposite. The results obtained using this model show that the wood cell wall material under shear loading deforms in an elastic and then plastic manner. The plastic regime can be divided into two parts according to the different deformation mechanisms: yielding of the matrix and sliding of matrix along the cellulose surface. Our molecular dynamics study provides insights of the mechanical behavior of wood cell wall material at the molecular level, and paves a way for the multi-scale understanding of the mechanical properties of wood. Copyright © 2014 Elsevier Ltd. All rights reserved.
Elucidating the Physical and Chemical Structural Changes of Proteins on Clay Mineral Surfaces using Large-scale Molecular Dynamics Simulations in Tandem with NMR Spectroscopy

NASA Astrophysics Data System (ADS)

Andersen, A.; Govind, N.; Washton, N.; Reardon, P.; Chacon, S. S.; Burton, S.; Lipton, A.; Kleber, M.; Qafoku, N. P.

2014-12-01

Carbon cycling among the three major Earth's pools, i.e., atmosphere, terrestrial systems and oceans, has received increased attention because the concentration of CO2 in the atmosphere has increased significantly in recent years reaching concentrations greater than 400 ppm that have never been recorded before, warming the planet and changing the climate. Within the terrestrial system, soil organic matter (SOM) represents an important sub-pool of carbon. The associations of SOM with soil mineral interfaces and particles, creating micro-aggregates, are believed to regulate the bioavailability of the associated organic carbon by protecting it from transformations and mineralization to carbon dioxide. Nevertheless, the molecular scale interactions of different types of SOM with a variety of soil minerals and the controls on the extent and rate of SOM transformation and mineralization are not well documented in the current literature. Given the importance of SOM fate and persistence in soils and the current knowledge gaps, the application of atomistic scale simulations to study SOM/mineral associations in abiotic model systems offers rich territory for original and impactful science. Molecular modeling and simulation of SOM is a burgeoning and challenging avenue for aiding the characterization of these complex compounds and chemical systems and for studying their interactions in self-assembled aggregates composed of different organic matter compounds and with mineral surfaces of different types and common in soils, which are thought to contribute to their reactive properties including recalcitrance potential and resistance to mineralization. Here, we will discuss our large-scale molecular dynamics simulation efforts to explore the interaction of proteins with clay minerals (i.e., phyllosilicates such as kaolinite, smectite and micas), including the potential physical and chemical structural changes of proteins, protein adsorption by polar and permanently charged mineral surfaces and variably charged edges, and the potential role of amphiphilic proteins in providing adsorptive layers for SOM-mineral interfaces. Our efforts at characterizing these systems through combined modeling and simulation and NMR will also be discussed.
Molecular sorting by electrical steering of microtubules in kinesin-coated channels.

PubMed

van den Heuvel, Martin G L; de Graaff, Martijn P; Dekker, Cees

2006-05-12

Integration of biomolecular motors in nanoengineered structures raises the intriguing possibility of manipulating materials on nanometer scales. We have managed to integrate kinesin motor proteins in closed submicron channels and to realize active electrical control of the direction of individual kinesin-propelled microtubule filaments at Y junctions. Using this technique, we demonstrate molecular sorting of differently labeled microtubules. We attribute the steering of microtubules to electric field-induced bending of the leading tip. From measurements of the orientation-dependent electrophoretic motion of individual, freely suspended microtubules, we estimate the net applied force on the tip to be in the picoNewton range and we infer an effective charge of 12 e- per tubulin dimer under physiological conditions.
Nanotubule and Tour Molecule Based Molecular Electronics: Suggestion for a Hybrid Approach

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Saini, Subhash (Technical Monitor)

1998-01-01

Recent experimental and theoretical attempts and results indicate two distinct broad pathways towards future molecular electronic devices and architectures. The first is the approach via Tour type ladder molecules and their junctions which can be fabricated with solution phase chemical approaches. Second are fullerenes or nanotubules and their junctions which may have better conductance, switching and amplifying characteristics but can not be made through well controlled and defined chemical means. A hybrid approach combining the two pathways to take advantage of the characteristics of both is suggested. Dimension and scale of such devices would be somewhere in between isolated molecule and nanotubule based devices but it maybe possible to use self-assembly towards larger functional and logicalunits.
Nonlinear photoacoustic spectroscopy of hemoglobin

PubMed Central

Danielli, Amos; Maslov, Konstantin; Favazza, Christopher P.; Xia, Jun; Wang, Lihong V.

2015-01-01

As light intensity increases in photoacoustic imaging, the saturation of optical absorption and the temperature dependence of the thermal expansion coefficient result in a measurable nonlinear dependence of the photoacoustic (PA) signal on the excitation pulse fluence. Here, under controlled conditions, we investigate the intensity-dependent photoacoustic signals from oxygenated and deoxygenated hemoglobin at varied optical wavelengths and molecular concentrations. The wavelength and concentration dependencies of the nonlinear PA spectrum are found to be significantly greater in oxygenated hemoglobin than in deoxygenated hemoglobin. These effects are further influenced by the hemoglobin concentration. These nonlinear phenomena provide insights into applications of photoacoustics, such as measurements of average inter-molecular distances on a nm scale or with a tuned selection of wavelengths, a more accurate quantitative PA tomography. PMID:26045627

Nonlinear photoacoustic spectroscopy of hemoglobin.

PubMed

Danielli, Amos; Maslov, Konstantin; Favazza, Christopher P; Xia, Jun; Wang, Lihong V

2015-05-18

As light intensity increases in photoacoustic imaging, the saturation of optical absorption and the temperature dependence of the thermal expansion coefficient result in a measurable nonlinear dependence of the photoacoustic (PA) signal on the excitation pulse fluence. Here, under controlled conditions, we investigate the intensity-dependent photoacoustic signals from oxygenated and deoxygenated hemoglobin at varied optical wavelengths and molecular concentrations. The wavelength and concentration dependencies of the nonlinear PA spectrum are found to be significantly greater in oxygenated hemoglobin than in deoxygenated hemoglobin. These effects are further influenced by the hemoglobin concentration. These nonlinear phenomena provide insights into applications of photoacoustics, such as measurements of average inter-molecular distances on a nm scale or with a tuned selection of wavelengths, a more accurate quantitative PA tomography.
From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal.

PubMed

Zheng, Jianping; Birktoft, Jens J; Chen, Yi; Wang, Tong; Sha, Ruojie; Constantinou, Pamela E; Ginell, Stephan L; Mao, Chengde; Seeman, Nadrian C

2009-09-03

We live in a macroscopic three-dimensional (3D) world, but our best description of the structure of matter is at the atomic and molecular scale. Understanding the relationship between the two scales requires a bridge from the molecular world to the macroscopic world. Connecting these two domains with atomic precision is a central goal of the natural sciences, but it requires high spatial control of the 3D structure of matter. The simplest practical route to producing precisely designed 3D macroscopic objects is to form a crystalline arrangement by self-assembly, because such a periodic array has only conceptually simple requirements: a motif that has a robust 3D structure, dominant affinity interactions between parts of the motif when it self-associates, and predictable structures for these affinity interactions. Fulfilling these three criteria to produce a 3D periodic system is not easy, but should readily be achieved with well-structured branched DNA motifs tailed by sticky ends. Complementary sticky ends associate with each other preferentially and assume the well-known B-DNA structure when they do so; the helically repeating nature of DNA facilitates the construction of a periodic array. It is essential that the directions of propagation associated with the sticky ends do not share the same plane, but extend to form a 3D arrangement of matter. Here we report the crystal structure at 4 A resolution of a designed, self-assembled, 3D crystal based on the DNA tensegrity triangle. The data demonstrate clearly that it is possible to design and self-assemble a well-ordered macromolecular 3D crystalline lattice with precise control.
Tuning Adsorption Duration To Control the Diffusion of a Nanoparticle in Adsorbing Polymers.

PubMed

Cao, Xue-Zheng; Merlitz, Holger; Wu, Chen-Xu

2017-06-15

Controlling the nanoparticle (NP) diffusion in polymers is a prerequisite to obtain polymer nanocomposites (PNCs) with desired dynamical and rheological properties and to achieve targeted delivery of nanomedicine in biological systems. Here we determine the suppression mechanism of direct NP-polymer attraction to hamper the NP mobility in adsorbing polymers and then quantify the dependence of the effective viscosity η eff felt by the NP on the adsorption duration τ ads of polymers on the NP using scaling theory analysis and molecular dynamics simulations. We propose and confirm that participation of adsorbed chains in the NP motion break up at time intervals beyond τ ads due to the rearrangement of polymer segments at the NP surface, which accounts for the onset of Fickian NP diffusion on a time scale of t ≈ τ ads . We develop a power law, η eff ∼ (τ ads ) ν , where ν is the scaling exponent of the dependence of polymer coil size on the chain length, which leads to a theoretical basis for the design of PNCs and nanomedicine with desired applications through tuning the polymer adsorption duration.
A scaling law of radial gas distribution in disk galaxies

NASA Technical Reports Server (NTRS)

Wang, Zhong

1990-01-01

Based on the idea that local conditions within a galactic disk largely determine the region's evolution time scale, researchers built a theoretical model to take into account molecular cloud and star formations in the disk evolution process. Despite some variations that may be caused by spiral arms and central bulge masses, they found that many late-type galaxies show consistency with the model in their radial atomic and molecular gas profiles. In particular, researchers propose that a scaling law be used to generalize the gas distribution characteristics. This scaling law may be useful in helping to understand the observed gas contents in many galaxies. Their model assumes an exponential mass distribution with disk radius. Most of the mass are in atomic gas state at the beginning of the evolution. Molecular clouds form through a modified Schmidt Law which takes into account gravitational instabilities in a possible three-phase structure of diffuse interstellar medium (McKee and Ostriker, 1977; Balbus and Cowie, 1985); whereas star formation proceeds presumably unaffected by the environmental conditions outside of molecular clouds (Young, 1987). In such a model both atomic and molecular gas profiles in a typical galactic disk (as a result of the evolution) can be fitted simultaneously by adjusting the efficiency constants. Galaxies of different sizes and masses, on the other hand, can be compared with the model by simply scaling their characteristic length scales and shifting their radial ranges to match the assumed disk total mass profile sigma tot(r).
Molecular diagnosis of Plasmodium ovale by photo-induced electron transfer fluorogenic primers: PET-PCR

PubMed Central

Akerele, David; Ljolje, Dragan; Talundzic, Eldin; Udhayakumar, Venkatachalam

2017-01-01

Accurate diagnosis of malaria infections continues to be challenging and elusive, especially in the detection of submicroscopic infections. Developing new malaria diagnostic tools that are sensitive enough to detect low-level infections, user friendly, cost effective and capable of performing large scale diagnosis, remains critical. We have designed novel self-quenching photo-induced electron transfer (PET) fluorogenic primers for the detection of P. ovale by real-time PCR. In our study, a total of 173 clinical samples, consisting of different malaria species, were utilized to test this novel PET-PCR primer. The sensitivity and specificity were calculated using nested-PCR as the reference test. The novel primer set demonstrated a sensitivity of 97.5% and a specificity of 99.2% (95% CI 85.2–99.8% and 95.2–99.9% respectively). Furthermore, the limit of detection for P. ovale was found to be 1 parasite/μl. The PET-PCR assay is a new molecular diagnostic tool with comparable performance to other commonly used PCR methods. It is relatively easy to perform, and amiable to large scale malaria surveillance studies and malaria control and elimination programs. Further field validation of this novel primer will be helpful to ascertain the utility for large scale malaria screening programs. PMID:28640824
Molecular diagnosis of Plasmodium ovale by photo-induced electron transfer fluorogenic primers: PET-PCR.

PubMed

Akerele, David; Ljolje, Dragan; Talundzic, Eldin; Udhayakumar, Venkatachalam; Lucchi, Naomi W

2017-01-01

Accurate diagnosis of malaria infections continues to be challenging and elusive, especially in the detection of submicroscopic infections. Developing new malaria diagnostic tools that are sensitive enough to detect low-level infections, user friendly, cost effective and capable of performing large scale diagnosis, remains critical. We have designed novel self-quenching photo-induced electron transfer (PET) fluorogenic primers for the detection of P. ovale by real-time PCR. In our study, a total of 173 clinical samples, consisting of different malaria species, were utilized to test this novel PET-PCR primer. The sensitivity and specificity were calculated using nested-PCR as the reference test. The novel primer set demonstrated a sensitivity of 97.5% and a specificity of 99.2% (95% CI 85.2-99.8% and 95.2-99.9% respectively). Furthermore, the limit of detection for P. ovale was found to be 1 parasite/μl. The PET-PCR assay is a new molecular diagnostic tool with comparable performance to other commonly used PCR methods. It is relatively easy to perform, and amiable to large scale malaria surveillance studies and malaria control and elimination programs. Further field validation of this novel primer will be helpful to ascertain the utility for large scale malaria screening programs.
A nanometre-scale electronic switch consisting of a metal cluster and redox-addressable groups.

PubMed

Gittins, D I; Bethell, D; Schiffrin, D J; Nichols, R J

2000-11-02

So-called bottom-up fabrication methods aim to assemble and integrate molecular components exhibiting specific functions into electronic devices that are orders of magnitude smaller than can be fabricated by lithographic techniques. Fundamental to the success of the bottom-up approach is the ability to control electron transport across molecular components. Organic molecules containing redox centres-chemical species whose oxidation number, and hence electronic structure, can be changed reversibly-support resonant tunnelling and display promising functional behaviour when sandwiched as molecular layers between electrical contacts, but their integration into more complex assemblies remains challenging. For this reason, functionalized metal nanoparticles have attracted much interest: they exhibit single-electron characteristics (such as quantized capacitance charging) and can be organized through simple self-assembly methods into well ordered structures, with the nanoparticles at controlled locations. Here we report scanning tunnelling microscopy measurements showing that organic molecules containing redox centres can be used to attach metal nanoparticles to electrode surfaces and so control the electron transport between them. Our system consists of gold nanoclusters a few nanometres across and functionalized with polymethylene chains that carry a central, reversibly reducible bipyridinium moiety. We expect that the ability to electronically contact metal nanoparticles via redox-active molecules, and to alter profoundly their tunnelling properties by charge injection into these molecules, can form the basis for a range of nanoscale electronic switches.
Boolean Logic Tree of Label-Free Dual-Signal Electrochemical Aptasensor System for Biosensing, Three-State Logic Computation, and Keypad Lock Security Operation.

PubMed

Lu, Jiao Yang; Zhang, Xin Xing; Huang, Wei Tao; Zhu, Qiu Yan; Ding, Xue Zhi; Xia, Li Qiu; Luo, Hong Qun; Li, Nian Bing

2017-09-19

The most serious and yet unsolved problems of molecular logic computing consist in how to connect molecular events in complex systems into a usable device with specific functions and how to selectively control branchy logic processes from the cascading logic systems. This report demonstrates that a Boolean logic tree is utilized to organize and connect "plug and play" chemical events DNA, nanomaterials, organic dye, biomolecule, and denaturant for developing the dual-signal electrochemical evolution aptasensor system with good resettability for amplification detection of thrombin, controllable and selectable three-state logic computation, and keypad lock security operation. The aptasensor system combines the merits of DNA-functionalized nanoamplification architecture and simple dual-signal electroactive dye brilliant cresyl blue for sensitive and selective detection of thrombin with a wide linear response range of 0.02-100 nM and a detection limit of 1.92 pM. By using these aforementioned chemical events as inputs and the differential pulse voltammetry current changes at different voltages as dual outputs, a resettable three-input biomolecular keypad lock based on sequential logic is established. Moreover, the first example of controllable and selectable three-state molecular logic computation with active-high and active-low logic functions can be implemented and allows the output ports to assume a high impediment or nothing (Z) state in addition to the 0 and 1 logic levels, effectively controlling subsequent branchy logic computation processes. Our approach is helpful in developing the advanced controllable and selectable logic computing and sensing system in large-scale integration circuits for application in biomedical engineering, intelligent sensing, and control.
An ignition key for atomic-scale engines

NASA Astrophysics Data System (ADS)

Dundas, Daniel; Cunningham, Brian; Buchanan, Claire; Terasawa, Asako; Paxton, Anthony T.; Todorov, Tchavdar N.

2012-10-01

A current-carrying resonant nanoscale device, simulated by non-adiabatic molecular dynamics, exhibits sharp activation of non-conservative current-induced forces with bias. The result, above the critical bias, is generalized rotational atomic motion with a large gain in kinetic energy. The activation exploits sharp features in the electronic structure, and constitutes, in effect, an ignition key for atomic-scale motors. A controlling factor for the effect is the non-equilibrium dynamical response matrix for small-amplitude atomic motion under current. This matrix can be found from the steady-state electronic structure by a simpler static calculation, providing a way to detect the likely appearance, or otherwise, of non-conservative dynamics, in advance of real-time modelling.
The molecular gradient using the divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation theory: The DEC-RI-MP2 gradient

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bykov, Dmytro; Kristensen, Kasper; Kjærgaard, Thomas

We report an implementation of the molecular gradient using the divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation theory (DEC-RI-MP2). The new DEC-RI-MP2 gradient method combines the precision control as well as the linear-scaling and massively parallel features of the DEC scheme with efficient evaluations of the gradient contributions using the RI approximation. We further demonstrate that the DEC-RI-MP2 gradient method is capable of calculating molecular gradients for very large molecular systems. A test set of supramolecular complexes containing up to 158 atoms and 1960 contracted basis functions has been employed to demonstrate the general applicability of the DEC-RI-MP2 methodmore » and to analyze the errors of the DEC approximation. Moreover, the test set contains molecules of complicated electronic structures and is thus deliberately chosen to stress test the DEC-RI-MP2 gradient implementation. Additionally, as a showcase example the full molecular gradient for insulin (787 atoms and 7604 contracted basis functions) has been evaluated.« less
New single-copy nuclear genes for scale insect systematics

USDA-ARS?s Scientific Manuscript database

Despite the advent of next-generation sequencing, the polymerase chain reaction (PCR) and Sanger sequencing remain useful tools for molecular identification and systematics. To date, molecular systematics of scale insects has been constrained by the paucity of loci that researchers have been able to...
Model development and verification for mass transport to Escherichia coli cells in a turbulent flow

NASA Astrophysics Data System (ADS)

Hondzo, Miki; Al-Homoud, Amer

2007-08-01

Theoretical studies imply that fluid motion does not significantly increase the molecular diffusive mass flux toward and away from microscopic organisms. This study presents experimental and theoretical evidence that small-scale turbulence modulates enhanced mass transport to Escherichia coli cells in a turbulent flow. Using the technique of inner region and outer region expansions, a model for dissolved oxygen and glucose uptake by E. coli was developed. The mass transport to the E. coli was modeled by the Sherwood (Sh)-Péclet (Pe) number relationship with redefined characteristic length and velocity scales. The model Sh = (1 + Pe1/2 + Pe) agreed with the laboratory measurements well. The Péclet number that quantifies the role and function of small-scale turbulence on E. coli metabolism is defined by Pe = (?) where Ezz is the root mean square of fluid extension in the direction of local vorticity, ηK is the Kolmogorov length scale, Lc is the length scale of E. coli, and D is the molecular diffusion coefficient. An alternative formulation for the redefined Pe is given by Pe = (?) where ? = 0.5(ɛν)1/4 is the Kolmogorov velocity averaged over the Kolmogorov length scale, ɛ is dissipation of turbulent kinetic energy, and ν is the kinematic viscosity of fluid. The dissipation of turbulent kinetic energy was estimated directly from measured velocity gradients and was within the reported range in engineered and natural aquatic ecosytems. The specific growth of E. coli was up to 5 times larger in a turbulent flow in comparison to the still water controls. Dissolved oxygen and glucose uptake were enhanced with increased ɛ in the turbulent flow.
Physical models have gender-specific effects on student understanding of protein structure-function relationships.

PubMed

Forbes-Lorman, Robin M; Harris, Michelle A; Chang, Wesley S; Dent, Erik W; Nordheim, Erik V; Franzen, Margaret A

2016-07-08

Understanding how basic structural units influence function is identified as a foundational/core concept for undergraduate biological and biochemical literacy. It is essential for students to understand this concept at all size scales, but it is often more difficult for students to understand structure-function relationships at the molecular level, which they cannot as effectively visualize. Students need to develop accurate, 3-dimensional mental models of biomolecules to understand how biomolecular structure affects cellular functions at the molecular level, yet most traditional curricular tools such as textbooks include only 2-dimensional representations. We used a controlled, backward design approach to investigate how hand-held physical molecular model use affected students' ability to logically predict structure-function relationships. Brief (one class period) physical model use increased quiz score for females, whereas there was no significant increase in score for males using physical models. Females also self-reported higher learning gains in their understanding of context-specific protein function. Gender differences in spatial visualization may explain the gender-specific benefits of physical model use observed. © 2016 The Authors Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 44(4):326-335, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.
Soft matter interactions at the molecular scale: interaction forces and energies between single hydrophobic model peptides.

PubMed

Stock, Philipp; Utzig, Thomas; Valtiner, Markus

2017-02-08

In all realms of soft matter research a fundamental understanding of the structure/property relationships based on molecular interactions is crucial for developing a framework for the targeted design of soft materials. However, a molecular picture is often difficult to ascertain and yet essential for understanding the many different competing interactions at play, including entropies and cooperativities, hydration effects, and the enormous design space of soft matter. Here, we characterized for the first time the interaction between single hydrophobic molecules quantitatively using atomic force microscopy, and demonstrated that single molecular hydrophobic interaction free energies are dominated by the area of the smallest interacting hydrophobe. The interaction free energy amounts to 3-4 kT per hydrophobic unit. Also, we find that the transition state of the hydrophobic interactions is located at 3 Å with respect to the ground state, based on Bell-Evans theory. Our results provide a new path for understanding the nature of hydrophobic interactions at the single molecular scale. Our approach enables us to systematically vary hydrophobic and any other interaction type by utilizing peptide chemistry providing a strategic advancement to unravel molecular surface and soft matter interactions at the single molecular scale.
High Performance Parallel Computational Nanotechnology

NASA Technical Reports Server (NTRS)

Saini, Subhash; Craw, James M. (Technical Monitor)

1995-01-01

At a recent press conference, NASA Administrator Dan Goldin encouraged NASA Ames Research Center to take a lead role in promoting research and development of advanced, high-performance computer technology, including nanotechnology. Manufacturers of leading-edge microprocessors currently perform large-scale simulations in the design and verification of semiconductor devices and microprocessors. Recently, the need for this intensive simulation and modeling analysis has greatly increased, due in part to the ever-increasing complexity of these devices, as well as the lessons of experiences such as the Pentium fiasco. Simulation, modeling, testing, and validation will be even more important for designing molecular computers because of the complex specification of millions of atoms, thousands of assembly steps, as well as the simulation and modeling needed to ensure reliable, robust and efficient fabrication of the molecular devices. The software for this capacity does not exist today, but it can be extrapolated from the software currently used in molecular modeling for other applications: semi-empirical methods, ab initio methods, self-consistent field methods, Hartree-Fock methods, molecular mechanics; and simulation methods for diamondoid structures. In as much as it seems clear that the application of such methods in nanotechnology will require powerful, highly powerful systems, this talk will discuss techniques and issues for performing these types of computations on parallel systems. We will describe system design issues (memory, I/O, mass storage, operating system requirements, special user interface issues, interconnects, bandwidths, and programming languages) involved in parallel methods for scalable classical, semiclassical, quantum, molecular mechanics, and continuum models; molecular nanotechnology computer-aided designs (NanoCAD) techniques; visualization using virtual reality techniques of structural models and assembly sequences; software required to control mini robotic manipulators for positional control; scalable numerical algorithms for reliability, verifications and testability. There appears no fundamental obstacle to simulating molecular compilers and molecular computers on high performance parallel computers, just as the Boeing 777 was simulated on a computer before manufacturing it.
The Role of Magnetic Fields in Star Formation

NASA Astrophysics Data System (ADS)

Pipher, Judith

2018-06-01

The SOFIA instrument complement makes available the capability to characterize the physical properties (turbulence, dynamics, magnetic field structure and strength, gas density) of the molecular cloud filaments in which stars form.HAWC+, the newest SOFIA instrument, provides a unique opportunity to probe the complex roles that magnetic fields play in the star formation process on spatial scales intermediate to those explored by Planck (5’ scale), to those of ALMA at the smallest spatial scales (<0.6”scale and 2” fields of view). HAWC+ measures the thermal emission from dust grains in molecular cloud star forming regions at wavelengths 53 to 216 mm, as well as the far infrared polarization on diffraction-limited spatial scales of 5” – 20” over fields of view ~2’ – 8’. Complementary near- to mid-IR polarimetry on 8-10m telescopes is available, as is submm polarimetry from both ground-based and balloon-borne telescopes. Currently there is no other far-IR polarimetry facility, and the HAWC+ wavelength ranges allow discrimination among different polarization mechanisms. HAWC+’ angular resolution is particularly well suited to study the magnetic field of entire cloud cores, thus connecting the Planck large scale molecular cloud structure with ALMA’s detailed small-scale structure of the core.SOFIA also offers the advantages of molecular line emission follow-up on regions for which HAWC+ determines magnetic field strength and direction. GREAT and/or FIFI-LS molecular line observations of the region of interest will complement the magnetic field observations: cloud and filament dynamics, the magnitude of the turbulence, and of course the core gas density can be determined through observations of appropriate molecular lines.These observations, as well as synergistic observations with other telescopes, will provide powerful tools to further our understanding of the fundamental physics of both low mass and high mass star formation, including the role that magnetic fields play in each.
Characterizing Low Molecular Weight Organic Matter in Arctic Polygonal Tundra Soils to Identify Biogeochemical Hotspots Using a Dual-Separation, High-Resolution Mass Spectrometry Approach

NASA Astrophysics Data System (ADS)

Ladd, M.; Wullschleger, S. D.; Iversen, C. M.; Hettich, R.

2016-12-01

Reliably modeling biogeochemical processes (e.g. decomposition, plant-microbial competition for nutrients) across spatial or temporal scales requires elucidating the chemical composition of low molecular weight (LMW) dissolved soil organic matter (DOM). Our understanding is limited, however, by the wide-ranging physicochemical properties and high fluxes of these compounds, posing major challenges in detection, isolation, and quantification. Here, we developed and evaluated a sensitive, non-targeted approach to characterize LMW DOM in the Arctic, a unique system that is warming at a rate twice that of the global average and may have significant feedbacks to global C and N cycles. Soil cores were collected from a continuous permafrost, polygonal tundra landscape near Barrow, Alaska (71° 16' N) and sectioned into 5 cm increments. Water and salt extracts from each section were filtered and injected onto C18 reversed-phase or zwitterionic-type hydrophilic interaction chromatography (ZIC-pHILIC) columns for separation. LMW DOM profiles were obtained using high-resolution mass spectrometry (HRMS), and unique features, known and unknown, were characterized by LC retention time, accurate mass (m/z), and molecular fragmentation pattern. Coupling two orthogonal chromatographic separations with HRMS enabled the characterization of hundreds of analytes in a single measurement providing enhanced, high-throughput coverage of LMW DOM from soil extracts. The complexity and relative/absolute intensities of LMW DOM features (e.g. organic acids, amino sugars, peptides) varied across polygon type (high- or low-centered), extract condition, and with depth, providing an information-rich, molecular signal of LMW DOM availability across scales. Comprehensively profiling this complex mixture of small molecules of both biotic and abiotic origin provides a chemical signature of biological function, allowing for more reliable predictions of how discrete, molecular-scale processes may control landscape dynamics. In the Arctic, this platform can be leveraged to identify biogeochemical hotspots to gain insight into to how warming temperatures will impact microbial dynamics and CO2 and CH4 fluxes from these systems.
Resolving molecular gas to ~500 pc in a unique star forming disk galaxy at z~2

NASA Astrophysics Data System (ADS)

Brisbin, Drew; Aravena, Manuel; Hodge, Jacqueline; Carilli, Chris Luke; Daddi, Emanuele; Dannerbauer, Helmut; Riechers, Dominik; Wagg, Jeff

2018-06-01

We have resolved molecular gas in a 'typical' star forming disk galaxy at z>2 down to the scale of ~500 pc. Previous observations of CO and [CI] lines on larger spatial scales have revealed bulk molecular and atomic gas properties indicating that the target is a massive disk galaxy with large gas reserves. Unlike many galaxies studied at high redshift, it is undergoing modest quiescent star formation rather than bursty centrally concentrated star formation. Therefore this galaxy represents an under-studied, but cosmologically important population in the early universe. Our new observations of CO (4-3) highlight the clumpy molecular gas fuelling star formation throughout the disk. Underlying continuum from cold dust provides a key constraint on star formation rate surface densities, allowing us to examine the star formation rate surface density scaling law in a never-before-tested regime of early universe galaxies.These observations enable an unprecedented view of the obscured star formation that is hidden to optical/UV imaging and trace molecular gas on a fine enough scale to resolve morphological traits and provide a view akin to single dish surveys in the local universe.
Multiple time step integrators in ab initio molecular dynamics.

PubMed

Luehr, Nathan; Markland, Thomas E; Martínez, Todd J

2014-02-28

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.
Vascular biology: cellular and molecular profiling.

PubMed

Baird, Alison E; Wright, Violet L

2006-02-01

Our understanding of the mechanisms underlying cerebrovascular atherosclerosis has improved in recent years, but significant gaps remain. New insights into the vascular biological processes that result in ischemic stroke may come from cellular and molecular profiling studies of the peripheral blood. In recent cellular profiling studies, increased levels of a proinflammatory T-cell subset (CD4 (+)CD28 (-)) have been associated with stroke recurrence and death. Expansion of this T-cell subset may occur after ischemic stroke and be a pathogenic mechanism leading to recurrent stroke and death. Increases in certain phenotypes of endothelial cell microparticles have been found in stroke patients relative to controls, possibly indicating a state of increased vascular risk. Molecular profiling approaches include gene expression profiling and proteomic methods that permit large-scale analyses of the transcriptome and the proteome, respectively. Ultimately panels of genes and proteins may be identified that are predictive of stroke risk. Cellular and molecular profiling studies of the peripheral blood and of atherosclerotic plaques may also pave the way for the development of therapeutic agents for primary and secondary stroke prevention.

Use of Molecular Dynamics Data in Biochemistry Courses: An Amphipathy Scale to Determine Protein [alpha]-Helix Transmembrane Segments

ERIC Educational Resources Information Center

Mazze, Fernanda M.; Fuzo, Carlos A.; Degreve, Leo; Ciancaglini, Pietro

2008-01-01

The aim of this manuscript is to explain the application of an amphipathy scale obtained from molecular dynamics simulations and to demonstrate how it can be useful in the protein structure field. It is shown that this scale is easy to be used with the advantage of revealing domains of transmembrane [alpha]-helix of proteins without the need of…
Control of the hierarchical assembly of π-conjugated optoelectronic peptides by pH and flow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mansbach, Rachael A.; Ferguson, Andrew L.

Self-assembled nanoaggregates of p-conjugated peptides possess optoelectronic properties due to electron delocalization over the conjugated peptide groups that make them attractive candidates for the fabrication of bioelectronic materials. We present a computational and theoretical study to resolve the microscopic effects of pH and flow on the non-equilibrium morphology and kinetics of early-stage assembly of an experimentally-realizable optoelectronic peptide that displays pH triggerable assembly. Employing coarse-grained molecular dynamics simulations, we probe the effects of pH on growth kinetics and aggregate morphology to show that control of the peptide protonation state by pH can be used to modulate the assembly rates, degreemore » of molecular alignment, and resulting morphologies within the self-assembling nanoaggregates. We also quantify the time and length scales at which convective flows employed in directed assembly compete with microscopic diffusion to show that flow influences cluster alignment and assembly rate during early-stage assembly only at extremely high shear rates. This suggests that observed improvements in optoelectronic properties at experimentally-accessible shear rates are due to the alignment of large aggregates of hundreds of monomers on time scales in excess of hundreds of nanoseconds. Lastly, our work provides new fundamental understanding of the effects of pH and flow to control the morphology and kinetics of early-stage assembly of p-conjugated peptides and lays the groundwork for the rational manipulation of environmental conditions to direct assembly and the attendant emergent optoelectronic properties.« less
Control of the hierarchical assembly of π-conjugated optoelectronic peptides by pH and flow

DOE PAGES

Mansbach, Rachael A.; Ferguson, Andrew L.

2017-01-01

Self-assembled nanoaggregates of p-conjugated peptides possess optoelectronic properties due to electron delocalization over the conjugated peptide groups that make them attractive candidates for the fabrication of bioelectronic materials. We present a computational and theoretical study to resolve the microscopic effects of pH and flow on the non-equilibrium morphology and kinetics of early-stage assembly of an experimentally-realizable optoelectronic peptide that displays pH triggerable assembly. Employing coarse-grained molecular dynamics simulations, we probe the effects of pH on growth kinetics and aggregate morphology to show that control of the peptide protonation state by pH can be used to modulate the assembly rates, degreemore » of molecular alignment, and resulting morphologies within the self-assembling nanoaggregates. We also quantify the time and length scales at which convective flows employed in directed assembly compete with microscopic diffusion to show that flow influences cluster alignment and assembly rate during early-stage assembly only at extremely high shear rates. This suggests that observed improvements in optoelectronic properties at experimentally-accessible shear rates are due to the alignment of large aggregates of hundreds of monomers on time scales in excess of hundreds of nanoseconds. Lastly, our work provides new fundamental understanding of the effects of pH and flow to control the morphology and kinetics of early-stage assembly of p-conjugated peptides and lays the groundwork for the rational manipulation of environmental conditions to direct assembly and the attendant emergent optoelectronic properties.« less
String-like collective motion in the α- and β-relaxation of a coarse-grained polymer melt

NASA Astrophysics Data System (ADS)

Pazmiño Betancourt, Beatriz A.; Starr, Francis W.; Douglas, Jack F.

2018-03-01

Relaxation in glass-forming liquids occurs as a multi-stage hierarchical process involving cooperative molecular motion. First, there is a "fast" relaxation process dominated by the inertial motion of the molecules whose amplitude grows upon heating, followed by a longer time α-relaxation process involving both large-scale diffusive molecular motion and momentum diffusion. Our molecular dynamics simulations of a coarse-grained glass-forming polymer melt indicate that the fast, collective motion becomes progressively suppressed upon cooling, necessitating large-scale collective motion by molecular diffusion for the material to relax approaching the glass-transition. In each relaxation regime, the decay of the collective intermediate scattering function occurs through collective particle exchange motions having a similar geometrical form, and quantitative relationships are derived relating the fast "stringlet" collective motion to the larger scale string-like collective motion at longer times, which governs the temperature-dependent activation energies associated with both thermally activated molecular diffusion and momentum diffusion.
Multi-level molecular modelling for plasma medicine

NASA Astrophysics Data System (ADS)

Bogaerts, Annemie; Khosravian, Narjes; Van der Paal, Jonas; Verlackt, Christof C. W.; Yusupov, Maksudbek; Kamaraj, Balu; Neyts, Erik C.

2016-02-01

Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma-biomolecule interactions.
Fluidic switching in nanochannels for the control of Inchworm: a synthetic biomolecular motor with a power stroke.

PubMed

Niman, Cassandra S; Zuckermann, Martin J; Balaz, Martina; Tegenfeldt, Jonas O; Curmi, Paul M G; Forde, Nancy R; Linke, Heiner

2014-12-21

Synthetic molecular motors typically take nanometer-scale steps through rectification of thermal motion. Here we propose Inchworm, a DNA-based motor that employs a pronounced power stroke to take micrometer-scale steps on a time scale of seconds, and we design, fabricate, and analyze the nanofluidic device needed to operate the motor. Inchworm is a kbp-long, double-stranded DNA confined inside a nanochannel in a stretched configuration. Motor stepping is achieved through externally controlled changes in salt concentration (changing the DNA's extension), coordinated with ligand-gated binding of the DNA's ends to the functionalized nanochannel surface. Brownian dynamics simulations predict that Inchworm's stall force is determined by its entropic spring constant and is ∼ 0.1 pN. Operation of the motor requires periodic cycling of four different buffers surrounding the DNA inside a nanochannel, while keeping constant the hydrodynamic load force on the DNA. We present a two-layer fluidic device incorporating 100 nm-radius nanochannels that are connected through a few-nm-wide slit to a microfluidic system used for in situ buffer exchanges, either diffusionally (zero flow) or with controlled hydrodynamic flow. Combining experiment with finite-element modeling, we demonstrate the device's key performance features and experimentally establish achievable Inchworm stepping times of the order of seconds or faster.
Final Report, University of California Merced: Uranium and strontium fate in waste-weathered sediments: Scaling of molecular processes to predict reactive transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chorover, Jon; Mueller, Karl; O'Day, Peggy Anne

2016-06-30

Objectives of the Project: 1. Determine the process coupling that occurs between mineral transformation and contaminant (U and Sr) speciation in acid-uranium waste weathered Hanford sediments. 2. Establish linkages between molecular-scale contaminant speciation and meso-scale contaminant lability, release and reactive transport. 3. Make conjunctive use of molecular- to bench-scale data to constrain the development of a mechanistic, reactive transport model that includes coupling of contaminant sorption-desorption and mineral transformation reactions. Hypotheses Tested: Uranium and strontium speciation in legacy sediments from the U-8 and U-12 Crib sites can be reproduced in bench-scale weathering experiments conducted on unimpacted Hanford sediments from themore » same formations; Reactive transport modeling of future uranium and strontium releases from the vadose zone of acid-waste weathered sediments can be effectively constrained by combining molecular-scale information on contaminant bonding environment with grain-scale information on contaminant phase partitioning, and meso-scale kinetic data on contaminant release from the waste-weathered porous media; Although field contamination and laboratory experiments differ in their diagenetic time scales (decades for field vs. months to years for lab), sediment dissolution, neophase nucleation, and crystal growth reactions that occur during the initial disequilibrium induced by waste-sediment interaction leave a strong imprint that persists over subsequent longer-term equilibration time scales and, therefore, give rise to long-term memory effects. Enabling Capabilities Developed: Our team developed an iterative measure-model approach that is broadly applicable to elucidate the mechanistic underpinnings of reactive contaminant transport in geomedia subject to active weathering.« less
A genomic regulatory network for development

NASA Technical Reports Server (NTRS)

Davidson, Eric H.; Rast, Jonathan P.; Oliveri, Paola; Ransick, Andrew; Calestani, Cristina; Yuh, Chiou-Hwa; Minokawa, Takuya; Amore, Gabriele; Hinman, Veronica; Arenas-Mena, Cesar;

2002-01-01

Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time.

Posttraumatic Stress Disorder and Depression Symptom Severities Are Differentially Associated With Hippocampal Subfield Volume Loss in Combat Veterans.

PubMed

Averill, Christopher L; Satodiya, Ritvij M; Scott, J Cobb; Wrocklage, Kristen M; Schweinsburg, Brian; Averill, Lynnette A; Akiki, Teddy J; Amoroso, Timothy; Southwick, Steven M; Krystal, John H; Abdallah, Chadi G

2017-01-01

Two decades of human neuroimaging research have associated volume reductions in the hippocampus with posttraumatic stress disorder. However, little is known about the distribution of volume loss across hippocampal subfields. Recent advances in neuroimaging methods have made it possible to accurately delineate 10 gray matter hippocampal subfields. Here, we apply a volumetric analysis of hippocampal subfields to data from a group of combat-exposed Veterans. Veterans (total, n = 68, posttraumatic stress disorder, n = 36; combat control, n = 32) completed high-resolution structural magnetic resonance imaging. Based on previously validated methods, hippocampal subfield volume measurements were conducted using FreeSurfer 6.0. The Clinician-Administered PTSD Scale assessed posttraumatic stress disorder symptom severity; Beck Depression Inventory assessed depressive symptom severity. Controlling for age and intracranial volume, partial correlation analysis examined the relationship between hippocampal subfields and symptom severity. Correction for multiple comparisons was performed using false discovery rate. Gender, intelligence, combat severity, comorbid anxiety, alcohol/substance use disorder, and medication status were investigated as potential confounds. In the whole sample, total hippocampal volume negatively correlated with Clinician-Administered PTSD Scale and Beck Depression Inventory scores. Of the 10 hippocampal subfields, Clinician-Administered PTSD Scale symptom severity negatively correlated with the hippocampus-amygdala transition area (HATA). Beck Depression Inventory scores negatively correlated with dentate gyrus, cornu ammonis 4 (CA4), HATA, CA2/3, molecular layer, and CA1. Follow-up analysis limited to the posttraumatic stress disorder group showed a negative correlation between Clinician-Administered PTSD Scale symptom severity and each of HATA, CA2/3, molecular layer, and CA4. This study provides the first evidence relating posttraumatic stress disorder and depression symptoms to abnormalities in the HATA, an anterior hippocampal region highly connected to prefrontal-amygdala circuitry. Notably, dentate gyrus abnormalities were associated with depression severity but not posttraumatic stress disorder symptoms. Future confirmatory studies should determine the extent to which dentate gyrus volume can differentiate between posttraumatic stress disorder- and depression-related pathophysiology.
Biomedical Diagnostics Using Manmade Nanostructures Integrated With Biomolecules

NASA Astrophysics Data System (ADS)

Wu, Tsai-Chin

There has been extensive research done on the bioengineering applications of nanoparticles. This thesis extended that work and focused on the application of semiconductor nanoparticles specifically as nano-scale detectors. By integrating two novel nanomaterial components, quantum dots and aptamers, nano-scale detectors may be fabricated. These nano-scale detectors make systematic studies on the molecular level possible and have other advantages described in the thesis. The analytes for such nanobiosensors include ions, cells, oligonucleotides, peptides or proteins. In this research, foodborne pathogens and potassium ions were chosen as the primary targets in the development of the nanosensors described in this thesis; due to their importance in the food industry and the biological sciences, respectively. More specifically, quantum dots were conjugated with short single-stranded nucleic acids and their fluorescence response was studied and evaluated to determine the viability of using them in nanoscale detector applications. To optimize the nanosensors, nano-scale spacer molecules are introduced at selected locations near the active regions of the nanosensors, and nanosensors synthesized with two different aptamer sequences were performed. The nanosensors were then tested with different ions and in real biological fluids; the results indicated that these nanosensors have promising potential applications in both self-diagnostics devices and molecular biological science research. The electrophoresis behavior and Raman spectra of these conjugations were also studied to examine these conjugations, in efforts to achieve better control over the proportional compositions of the entities that form these nanostructures. Several electrokinetic behavior dependencies on the nanoconjugations were observed and examined with double layer theory. This thesis investigated this novel nanobiosensor thoroughly from probe construction, performance evaluation, optical property characterization, to possible quality control methods. This research emphasized the fabrication of nano-detectors and provided a model to fabricate nano-detectors for a wide range of analytes by selecting appropriate aptamers and linker molecules.
Sequential Release of Proteins from Structured Multishell Microcapsules.

PubMed

Shimanovich, Ulyana; Michaels, Thomas C T; De Genst, Erwin; Matak-Vinkovic, Dijana; Dobson, Christopher M; Knowles, Tuomas P J

2017-10-09

In nature, a wide range of functional materials is based on proteins. Increasing attention is also turning to the use of proteins as artificial biomaterials in the form of films, gels, particles, and fibrils that offer great potential for applications in areas ranging from molecular medicine to materials science. To date, however, most such applications have been limited to single component materials despite the fact that their natural analogues are composed of multiple types of proteins with a variety of functionalities that are coassembled in a highly organized manner on the micrometer scale, a process that is currently challenging to achieve in the laboratory. Here, we demonstrate the fabrication of multicomponent protein microcapsules where the different components are positioned in a controlled manner. We use molecular self-assembly to generate multicomponent structures on the nanometer scale and droplet microfluidics to bring together the different components on the micrometer scale. Using this approach, we synthesize a wide range of multiprotein microcapsules containing three well-characterized proteins: glucagon, insulin, and lysozyme. The localization of each protein component in multishell microcapsules has been detected by labeling protein molecules with different fluorophores, and the final three-dimensional microcapsule structure has been resolved by using confocal microscopy together with image analysis techniques. In addition, we show that these structures can be used to tailor the release of such functional proteins in a sequential manner. Moreover, our observations demonstrate that the protein release mechanism from multishell capsules is driven by the kinetic control of mass transport of the cargo and by the dissolution of the shells. The ability to generate artificial materials that incorporate a variety of different proteins with distinct functionalities increases the breadth of the potential applications of artificial protein-based materials and provides opportunities to design more refined functional protein delivery systems.
Reviews and syntheses: Four decades of modeling methane cycling in terrestrial ecosystems

NASA Astrophysics Data System (ADS)

Xu, Xiaofeng; Yuan, Fengming; Hanson, Paul J.; Wullschleger, Stan D.; Thornton, Peter E.; Riley, William J.; Song, Xia; Graham, David E.; Song, Changchun; Tian, Hanqin

2016-06-01

Over the past 4 decades, a number of numerical models have been developed to quantify the magnitude, investigate the spatial and temporal variations, and understand the underlying mechanisms and environmental controls of methane (CH4) fluxes within terrestrial ecosystems. These CH4 models are also used for integrating multi-scale CH4 data, such as laboratory-based incubation and molecular analysis, field observational experiments, remote sensing, and aircraft-based measurements across a variety of terrestrial ecosystems. Here we summarize 40 terrestrial CH4 models to characterize their strengths and weaknesses and to suggest a roadmap for future model improvement and application. Our key findings are that (1) the focus of CH4 models has shifted from theoretical to site- and regional-level applications over the past 4 decades, (2) large discrepancies exist among models in terms of representing CH4 processes and their environmental controls, and (3) significant data-model and model-model mismatches are partially attributed to different representations of landscape characterization and inundation dynamics. Three areas for future improvements and applications of terrestrial CH4 models are that (1) CH4 models should more explicitly represent the mechanisms underlying land-atmosphere CH4 exchange, with an emphasis on improving and validating individual CH4 processes over depth and horizontal space, (2) models should be developed that are capable of simulating CH4 emissions across highly heterogeneous spatial and temporal scales, particularly hot moments and hotspots, and (3) efforts should be invested to develop model benchmarking frameworks that can easily be used for model improvement, evaluation, and integration with data from molecular to global scales. These improvements in CH4 models would be beneficial for the Earth system models and further simulation of climate-carbon cycle feedbacks.
Waveform control of orientation-dependent ionization of DCl in few-cycle laser fields.

PubMed

Znakovskaya, I; von den Hoff, P; Schirmel, N; Urbasch, G; Zherebtsov, S; Bergues, B; de Vivie-Riedle, R; Weitzel, K-M; Kling, M F

2011-05-21

Strong few-cycle light fields with stable electric field waveforms allow controlling electrons on time scales down to the attosecond domain. We have studied the dissociative ionization of randomly oriented DCl in 5 fs light fields at 720 nm in the tunneling regime. Momentum distributions of D(+) and Cl(+) fragments were recorded via velocity-map imaging. A waveform-dependent anti-correlated directional emission of D(+) and Cl(+) fragments is observed. Comparison of our results with calculations indicates that tailoring of the light field via the carrier envelope phase permits the control over the orientation of DCl(+) and in turn the directional emission of charged fragments upon the breakup of the molecular ion. © The Owner Societies 2011
A Scalable O(N) Algorithm for Large-Scale Parallel First-Principles Molecular Dynamics Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

2014-01-01

Traditional algorithms for first-principles molecular dynamics (FPMD) simulations only gain a modest capability increase from current petascale computers, due to their O(N 3) complexity and their heavy use of global communications. To address this issue, we are developing a truly scalable O(N) complexity FPMD algorithm, based on density functional theory (DFT), which avoids global communications. The computational model uses a general nonorthogonal orbital formulation for the DFT energy functional, which requires knowledge of selected elements of the inverse of the associated overlap matrix. We present a scalable algorithm for approximately computing selected entries of the inverse of the overlap matrix,more » based on an approximate inverse technique, by inverting local blocks corresponding to principal submatrices of the global overlap matrix. The new FPMD algorithm exploits sparsity and uses nearest neighbor communication to provide a computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic orbitals are confined, and a cutoff beyond which the entries of the overlap matrix can be omitted when computing selected entries of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to O(100K) atoms on O(100K) processors, with a wall-clock time of O(1) minute per molecular dynamics time step.« less
Digging Deeper: Development and evaluation of an untargeted metabolomics approach to identify biogeochemical hotspots with depth and by vegetation type in Arctic tundra soils

NASA Astrophysics Data System (ADS)

Ladd, M.; Wullschleger, S.; Hettich, R.

2017-12-01

Elucidating the chemical composition of low molecular weight (LMW) dissolved organic matter (DOM), and monitoring how this bioavailable pool varies over space and time, is critical to understanding the controlling mechanisms that underlie carbon release and storage in Arctic systems. Due to analytical challenges however, relatively little is known about how this complex mixture of small molecules varies with soil depth or how it may be influenced by vegetation. In this study, we evaluated an untargeted metabolomics approach for the characterization of LMW DOM in water extracts, and applied this approach in soil cores (10-cm diam., 30-cm depth), obtained near Barrow, Alaska (71° 16' N) from the organic-rich active layer where the aboveground vegetation was primarily either Carex aquatilis or Eriophorum angustifolium, two species commonly found in tundra systems. We hypothesized that by using a discovery-based approach, spatial patterns of chemical diversity could be identified, enabling the detection of biogeochemical hotspots across scales. LMW DOM profiles from triplicate water extracts were characterized using dual-separation, nano-liquid chromatography (LC) coupled to an electrospray Orbitrap mass spectrometer in positive and negative ion modes. Both LC separations—reversed-phase and hydrophilic interaction chromatography—were achieved with gradient elutions in 15 minutes. Using a precursor and fragment mass measurement accuracy of <5 ppm for singly charged ions, unique features not observed in the blank or control were compared across all samples. Statistically significant differences with depth and between vegetation were determined, and the resulting list of features was matched to online databases. Annotated classes of LMW DOM included plant and microbial metabolites, organic acids, osmolytes, sugars, and simple peptides. Based on the chemical profile, we were able to distinguish between samples at each depth and between vegetation types, suggesting that a molecularly-resolved, data-driven approach could allow for more reliable predictions of how biogeochemical processes occurring at the molecular-scale (e.g. plant-microbial competition for organic nutrients) impact carbon fluxes in the Arctic at the landscape-scale.
Effect of Particle Size and Impact Velocity on Collision Behaviors Between Nano-Scale TiN Particles: MD Simulation.

PubMed

Yao, Hai-Long; Hu, Xiao-Zhen; Yang, Guan-Jun

2018-06-01

Inter-particle bonding formation which determines qualities of nano-scale ceramic coatings is influenced by particle collision behaviors during high velocity collision processes. In this study, collision behaviors between nano-scale TiN particles with different diameters were illuminated by using Molecular Dynamics simulation through controlling impact velocities. Results show that nano-scale TiN particles exhibit three states depending on particle sizes and impact velocities, i.e., bonding, bonding with localized fracturing, and rebounding. These TiN particles states are summarized into a parameter selection map providing an overview of the conditions in terms of particle sizes and velocities. Microstructure results show that localized atoms displacement and partial fracture around the impact region are main reasons for bonding formation of nano-scale ceramic particles, which shows differences from conventional particles refining and amorphization. A relationship between the adhesion energy and the rebound energy is established to understand bonding formation mechanism for nano-scale TiN particle collision. Results show that the energy relationship is depended on the particle sizes and impact velocities, and nano-scale ceramic particles can be bonded together as the adhesion energy being higher than the rebound energy.
Canonical-ensemble extended Lagrangian Born-Oppenheimer molecular dynamics for the linear scaling density functional theory.

PubMed

Hirakawa, Teruo; Suzuki, Teppei; Bowler, David R; Miyazaki, Tsuyoshi

2017-10-11

We discuss the development and implementation of a constant temperature (NVT) molecular dynamics scheme that combines the Nosé-Hoover chain thermostat with the extended Lagrangian Born-Oppenheimer molecular dynamics (BOMD) scheme, using a linear scaling density functional theory (DFT) approach. An integration scheme for this canonical-ensemble extended Lagrangian BOMD is developed and discussed in the context of the Liouville operator formulation. Linear scaling DFT canonical-ensemble extended Lagrangian BOMD simulations are tested on bulk silicon and silicon carbide systems to evaluate our integration scheme. The results show that the conserved quantity remains stable with no systematic drift even in the presence of the thermostat.
Crystallization-driven assembly of conjugated-polymer-based nanostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayward, Ryan C.

2016-10-15

The goal of this project has been to improve our ability to simultaneously control the organization, and therefore the opto-electronic properties, of conjugated-polymer based materials across three different length-scales: 1) the molecular scale, in the sense of controlling growth and functionalization of highly crystalline semiconducting organic materials capable of efficient charge transport, 2) the nanoscale, in terms of positioning n- and p-type materials with domain sizes comparable to exciton diffusion lengths (~ 10 nm) to facilitate charge separation, and 3) the colloidal scale, such that well-defined crystalline nanoscale building blocks can be hierarchically organized into device layers. As described inmore » more detail below, the project was successful in generating powerful new approaches to, and improved fundamental understanding of, processing and self-assembly of organic and hybrid semiconducting materials across all three length-scales. Although the goals of the project were formulated with primarily photovoltaic architectures in mind, the outcomes of the project have significant implications for a variety of conjugated-polymer-based devices including field-effect-transistors for sensors and logic devices, as well as potentially thermoelectrics and battery electrode materials. The project has resulted in 10 peer-reviewed publications to date [1-10], with several additional manuscripts currently in preparation.« less
Nanopatterning of Group V Elements for Tailoring the Electronic Properties of Semiconductors by Monolayer Doping.

PubMed

Thissen, Peter; Cho, Kyeongjae; Longo, Roberto C

2017-01-18

Control of the electronic properties of semiconductors is primarily achieved through doping. While scaling down the device dimensions to the molecular regime presents an increasing number of difficulties, doping control at the nanoscale is still regarded as one of the major challenges of the electronic industry. Within this context, new techniques such as monolayer doping (MLD) represent a substantial improvement toward surface doping with atomic and specific doping dose control at the nanoscale. Our previous work has explained in detail the atomistic mechanism behind MLD by means of density-functional theory calculations (Chem. Mater. 2016, 28, 1975). Here, we address the key questions that will ultimately allow one to optimize the scalability of the MLD process. First, we show that dopant coverage control cannot be achieved by simultaneous reaction of several group V elements, but stepwise reactions make it possible. Second, using ab initio molecular dynamics, we investigate the thermal decomposition of the molecular precursors, together with the stability of the corresponding binary and ternary dopant oxides, prior to the dopant diffusion into the semiconductor surface. Finally, the effect of the coverage and type of dopant on the electronic properties of the semiconductor is also analyzed. Furthermore, the atomistic characterization of the MLD process raises unexpected questions regarding possible crystal damage effects by dopant exchange with the semiconductor ions or the final distribution of the doping impurities within the crystal structure. By combining all our results, optimization recipes to create ultrashallow doped junctions at the nanoscale are finally proposed.
A Kennicutt-Schmidt relation at molecular cloud scales and beyond

NASA Astrophysics Data System (ADS)

Khoperskov, Sergey A.; Vasiliev, Evgenii O.

2017-06-01

Using N-body/gasdynamic simulations of a Milky Way-like galaxy, we analyse a Kennicutt-Schmidt (KS) relation, Σ _SFR ∝ Σ _gas^N, at different spatial scales. We simulate synthetic observations in CO lines and ultraviolet (UV) band. We adopt the star formation rate (SFR) defined in two ways: based on free fall collapse of a molecular cloud - ΣSFR, cl, and calculated by using a UV flux calibration - ΣSFR,UV. We study a KS relation for spatially smoothed maps with effective spatial resolution from molecular cloud scales to several hundred parsecs. We find that for spatially and kinematically resolved molecular clouds the Σ _{SFR, cl} ∝ σ _{gas}^N relation follows the power law with index N ≈ 1.4. Using UV flux as SFR calibrator, we confirm a systematic offset between the ΣSFR,UV and Σgas distributions on scales compared to molecular cloud sizes. Degrading resolution of our simulated maps for surface densities of gas and SFRs, we establish that there is no relation ΣSFR,UV -Σgas below the resolution ˜50 pc. We find a transition range around scales ˜50-120 pc, where the power-law index N increases from 0 to 1-1.8 and saturates for scales larger ˜120 pc. A value of the index saturated depends on a surface gas density threshold and it becomes steeper for higher Σgas threshold. Averaging over scales with size of ≳ 150 pc the power-law index N equals 1.3-1.4 for surface gas density threshold ˜5 M⊙ pc-2. At scales ≳ 120 pc surface SFR densities determined by using CO data and UV flux, ΣSFR,UV/SFR, cl, demonstrate a discrepancy about a factor of 3. We argue that this may be originated from overestimating (constant) values of conversion factor, star formation efficiency or UV calibration used in our analysis.

Interferometric Mapping of Perseus Outflows with MASSES

NASA Astrophysics Data System (ADS)

Stephens, Ian; Dunham, Michael; Myers, Philip C.; MASSES Team

2017-01-01

The MASSES (Mass Assembly of Stellar Systems and their Evolution with the SMA) survey, a Submillimeter Array (SMA) large-scale program, is mapping molecular lines and continuum emission about the 75 known Class 0/I sources in the Perseus Molecular Cloud. In this talk, I present some of the key results of this project, with a focus on the CO(2-1) maps of the molecular outflows. In particular, I investigate how protostars inherit their rotation axes from large-scale magnetic fields and filamentary structure.
CCC7-119 Reactive Molecular Dynamics Simulations of Hot Spot Growth in Shocked Energetic Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, Aidan P.

2015-03-01

The purpose of this work is to understand how defects control initiation in energetic materials used in stockpile components; Sequoia gives us the core-count to run very large-scale simulations of up to 10 million atoms and; Using an OpenMP threaded implementation of the ReaxFF package in LAMMPS, we have been able to get good parallel efficiency running on 16k nodes of Sequoia, with 1 hardware thread per core.
Nonlinear photoacoustic spectroscopy of hemoglobin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Danielli, Amos; Maslov, Konstantin; Favazza, Christopher P.

2015-05-18

As light intensity increases in photoacoustic imaging, the saturation of optical absorption and the temperature dependence of the thermal expansion coefficient result in a measurable nonlinear dependence of the photoacoustic (PA) signal on the excitation pulse fluence. Here, under controlled conditions, we investigate the intensity-dependent photoacoustic signals from oxygenated and deoxygenated hemoglobin at varied optical wavelengths and molecular concentrations. The wavelength and concentration dependencies of the nonlinear PA spectrum are found to be significantly greater in oxygenated hemoglobin than in deoxygenated hemoglobin. These effects are further influenced by the hemoglobin concentration. These nonlinear phenomena provide insights into applications of photoacoustics,more » such as measurements of average inter-molecular distances on a nm scale or with a tuned selection of wavelengths, a more accurate quantitative PA tomography.« less
Easy design of colorimetric logic gates based on nonnatural base pairing and controlled assembly of gold nanoparticles.

PubMed

Zhang, Li; Wang, Zhong-Xia; Liang, Ru-Ping; Qiu, Jian-Ding

2013-07-16

Utilizing the principles of metal-ion-mediated base pairs (C-Ag-C and T-Hg-T), the pH-sensitive conformational transition of C-rich DNA strand, and the ligand-exchange process triggered by DL-dithiothreitol (DTT), a system of colorimetric logic gates (YES, AND, INHIBIT, and XOR) can be rationally constructed based on the aggregation of the DNA-modified Au NPs. The proposed logic operation system is simple, which consists of only T-/C-rich DNA-modified Au NPs, and it is unnecessary to exquisitely design and alter the DNA sequence for different multiple molecular logic operations. The nonnatural base pairing combined with unique optical properties of Au NPs promises great potential in multiplexed ion sensing, molecular-scale computers, and other computational logic devices.
Digital Microfluidics for Nucleic Acid Amplification

PubMed Central

Veigas, Bruno; Fortunato, Elvira; Martins, Rodrigo; Águas, Hugo; Igreja, Rui; Baptista, Pedro V.

2017-01-01

Digital Microfluidics (DMF) has emerged as a disruptive methodology for the control and manipulation of low volume droplets. In DMF, each droplet acts as a single reactor, which allows for extensive multiparallelization of biological and chemical reactions at a much smaller scale. DMF devices open entirely new and promising pathways for multiplex analysis and reaction occurring in a miniaturized format, thus allowing for healthcare decentralization from major laboratories to point-of-care with accurate, robust and inexpensive molecular diagnostics. Here, we shall focus on DMF platforms specifically designed for nucleic acid amplification, which is key for molecular diagnostics of several diseases and conditions, from pathogen identification to cancer mutations detection. Particular attention will be given to the device architecture, materials and nucleic acid amplification applications in validated settings. PMID:28672827
Histone underacetylation is an ancient component of mammalian X chromosome inactivation

PubMed Central

Wakefield, Matthew J.; Keohane, Ann M.; Turner, Bryan M.; Graves, Jennifer A. Marshall

1997-01-01

Underacetylation of histone H4 is thought to be involved in the molecular mechanism of mammalian X chromosome inactivation, which is an important model system for large-scale genetic control in eukaryotes. However, it has not been established whether histone underacetylation plays a critical role in the multistep inactivation pathway. Here we demonstrate differential histone H4 acetylation between the X chromosomes of a female marsupial, Macropus eugenii. Histone underacetylation is the only molecular aspect of X inactivation known to be shared by marsupial and eutherian mammals. Its strong evolutionary conservation implies that, unlike DNA methylation, histone underacetylation was a feature of dosage compensation in a common mammalian ancestor, and is therefore likely to play a central role in X chromosome inactivation in all mammals. PMID:9275180
Visualization and Interactivity in the Teaching of Chemistry to Science and Non-Science Students

ERIC Educational Resources Information Center

Venkataraman, Bhawani

2009-01-01

A series of interactive, instructional units have been developed that integrate computational molecular modelling and visualization to teach fundamental chemistry concepts and the relationship between the molecular and macro-scales. The units span the scale from atoms, small molecules to macromolecular systems, and introduce many of the concepts…
Self-assembly Controls Self-cleavage of HHR from ASBVd (-): a Combined SANS and Modeling Study

NASA Astrophysics Data System (ADS)

Leclerc, Fabrice; Zaccai, Giuseppe; Vergne, Jacques; Řìhovà, Martina; Martel, Anne; Maurel, Marie-Christine

2016-07-01

In the Avocado Sunblotch Viroid (ASBVd: 249-nt) from the Avsunviroidae family, a symmetric rolling-circle replication operates through an autocatalytic mechanism mediated by hammerhead ribozymes (HHR) embedded in both polarity strands. The concatenated multimeric ASBVd (+) and ASBVd (-) RNAs thus generated are processed by cleavage to unit-length where ASBVd (-) self-cleaves with more efficiency. Absolute scale small angle neutron scattering (SANS) revealed a temperature-dependent dimer association in both ASBVd (-) and its derived 79-nt HHR (-). A joint thermodynamic analysis of SANS and catalytic data indicates the rate-determining step corresponds to the dimer/monomer transition. 2D and 3D models of monomeric and dimeric HHR (-) suggest that the inter-molecular contacts stabilizing the dimer (between HI and HII domains) compete with the intra-molecular ones stabilizing the active conformation of the full-length HHR required for an efficient self-cleavage. Similar competing intra- and inter-molecular contacts are proposed in ASBVd (-) though with a remoter region from an extension of the HI domain.
A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

NASA Astrophysics Data System (ADS)

Ariey, Frédéric; Witkowski, Benoit; Amaratunga, Chanaki; Beghain, Johann; Langlois, Anne-Claire; Khim, Nimol; Kim, Saorin; Duru, Valentine; Bouchier, Christiane; Ma, Laurence; Lim, Pharath; Leang, Rithea; Duong, Socheat; Sreng, Sokunthea; Suon, Seila; Chuor, Char Meng; Bout, Denis Mey; Ménard, Sandie; Rogers, William O.; Genton, Blaise; Fandeur, Thierry; Miotto, Olivo; Ringwald, Pascal; Le Bras, Jacques; Berry, Antoine; Barale, Jean-Christophe; Fairhurst, Rick M.; Benoit-Vical, Françoise; Mercereau-Puijalon, Odile; Ménard, Didier

2014-01-01

Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide. To monitor the spread of artemisinin resistance, a molecular marker is urgently needed. Here, using whole-genome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia, we associate mutations in the PF3D7_1343700 kelch propeller domain (`K13-propeller') with artemisinin resistance in vitro and in vivo. Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent, and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia. Strong correlations between the presence of a mutant allele, in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance. K13-propeller polymorphism constitutes a useful molecular marker for large-scale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread.
A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

PubMed Central

Ariey, Frédéric; Witkowski, Benoit; Amaratunga, Chanaki; Beghain, Johann; Langlois, Anne-Claire; Khim, Nimol; Kim, Saorin; Duru, Valentine; Bouchier, Christiane; Ma, Laurence; Lim, Pharath; Leang, Rithea; Duong, Socheat; Sreng, Sokunthea; Suon, Seila; Chuor, Char Meng; Bout, Denis Mey; Ménard, Sandie; Rogers, William O.; Genton, Blaise; Fandeur, Thierry; Miotto, Olivo; Ringwald, Pascal; Le Bras, Jacques; Berry, Antoine; Barale, Jean-Christophe; Fairhurst, Rick M.; Benoit-Vical, Françoise; Mercereau-Puijalon, Odile; Ménard, Didier

2016-01-01

Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide. To monitor the spread of artemisinin resistance, a molecular marker is urgently needed. Here, using whole-genome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia, we associate mutations in the PF3D7_1343700 kelch propeller domain (‘K13-propeller’) with artemisinin resistance in vitro and in vivo. Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent, and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia. Strong correlations between the presence of a mutant allele, in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance. K13-propeller polymorphism constitutes a useful molecular marker for large-scale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread. PMID:24352242
Biomineralization-inspired synthesis of functional organic/inorganic hybrid materials: organic molecular control of self-organization of hybrids.

PubMed

Arakaki, Atsushi; Shimizu, Katsuhiko; Oda, Mayumi; Sakamoto, Takeshi; Nishimura, Tatsuya; Kato, Takashi

2015-01-28

Organisms produce various organic/inorganic hybrid materials, which are called biominerals. They form through the self-organization of organic molecules and inorganic elements under ambient conditions. Biominerals often have highly organized and hierarchical structures from nanometer to macroscopic length scales, resulting in their remarkable physical and chemical properties that cannot be obtained by simple accumulation of their organic and inorganic constituents. These observations motivate us to create novel functional materials exhibiting properties superior to conventional materials--both synthetic and natural. Herein, we introduce recent progress in understanding biomineralization processes at the molecular level and the development of organic/inorganic hybrid materials by these processes. We specifically outline fundamental molecular studies on silica, iron oxide, and calcium carbonate biomineralization and describe material synthesis based on these mechanisms. These approaches allow us to design a variety of advanced hybrid materials with desired morphologies, sizes, compositions, and structures through environmentally friendly synthetic routes using functions of organic molecules.
Ferroelectric molecular field-switch based on double proton transfer process: Static and dynamical simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rode, Michał F.; Sobolewski, Andrzej L.; Jankowska, Joanna

2016-04-07

In this work, we present a reversible ferroelectric molecular switch controlled by an external electric field. The studied (2Z)-1-(6-((Z)-2-hydroxy-2-phenylvinyl)pyridin-3-yl)-2-(pyridin-2(1H) -ylidene)ethanone (DSA) molecule is polarized by two uniaxial intramolecular hydrogen bonds. Two protons can be transferred along hydrogen bonds upon an electric field applied along the main molecular axis. The process results in reversion of the dipole moment of the system. Static ab initio and on-the-fly dynamical simulations of the DSA molecule placed in an external electric field give insight into the mechanism of the double proton transfer (DPT) in the system and allow for estimation of the time scale ofmore » this process. The results indicate that with increasing strength of the electric field, the step-wise mechanism of DPT changes into the downhill barrierless process in which the synchronous and asynchronous DPTs compete with each other.« less
Agent-Based Modeling in Molecular Systems Biology.

PubMed

Soheilypour, Mohammad; Mofrad, Mohammad R K

2018-07-01

Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.
Final Project Report: Release of aged contaminants from weathered sediments: Effects of sorbate speciation on scaling of reactive transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jon Chorover, University of Arizona; Peggy O'ÃÂÃÂDay, University of California, Merced; Karl Mueller, Penn State University

2012-10-01

Hanford sediments impacted by hyperalkaline high level radioactive waste have undergone incongruent silicate mineral weathering concurrent with contaminant uptake. In this project, we studied the impact of background pore water (BPW) on strontium, cesium and iodine desorption and transport in Hanford sediments that were experimentally weathered by contact with simulated hyperalkaline tank waste leachate (STWL) solutions. Using those lab-weathered Hanford sediments (HS) and model precipitates formed during nucleation from homogeneous STWL solutions (HN), we (i) provided detailed characterization of reaction products over a matrix of field-relevant gradients in contaminant concentration, PCO2, and reaction time; (ii) improved molecular-scale understanding of howmore » sorbate speciation controls contaminant desorption from weathered sediments upon removal of caustic sources; and (iii) developed a mechanistic, predictive model of meso- to field-scale contaminant reactive transport under these conditions.« less
Confined dynamics of grafted polymer chains in solutions of linear polymer

DOE PAGES

Poling-Skutvik, Ryan D.; Olafson, Katy N.; Narayanan, Suresh; ...

2017-09-11

Here, we measure the dynamics of high molecular weight polystyrene grafted to silica nanoparticles dispersed in semidilute solutions of linear polymer. Structurally, the linear free chains do not penetrate the grafted corona but increase the osmotic pressure of the solution, collapsing the grafted polymer and leading to eventual aggregation of the grafted particles at high matrix concentrations. Dynamically, the relaxations of the grafted polymer are controlled by the solvent viscosity according to the Zimm model on short time scales. On longer time scales, the grafted chains are confined by neighboring grafted chains, preventing full relaxation over the experimental time scale.more » Adding free linear polymer to the solution does not affect the initial Zimm relaxations of the grafted polymer but does increase the confinement of the grafted chains. Finally, our results elucidate the physics underlying the slow relaxations of grafted polymer.« less
Programming Self-Assembly of DNA Origami Honeycomb Two-Dimensional Lattices and Plasmonic Metamaterials.

PubMed

Wang, Pengfei; Gaitanaros, Stavros; Lee, Seungwoo; Bathe, Mark; Shih, William M; Ke, Yonggang

2016-06-22

Scaffolded DNA origami has proven to be a versatile method for generating functional nanostructures with prescribed sub-100 nm shapes. Programming DNA-origami tiles to form large-scale 2D lattices that span hundreds of nanometers to the micrometer scale could provide an enabling platform for diverse applications ranging from metamaterials to surface-based biophysical assays. Toward this end, here we design a family of hexagonal DNA-origami tiles using computer-aided design and demonstrate successful self-assembly of micrometer-scale 2D honeycomb lattices and tubes by controlling their geometric and mechanical properties including their interconnecting strands. Our results offer insight into programmed self-assembly of low-defect supra-molecular DNA-origami 2D lattices and tubes. In addition, we demonstrate that these DNA-origami hexagon tiles and honeycomb lattices are versatile platforms for assembling optical metamaterials via programmable spatial arrangement of gold nanoparticles (AuNPs) into cluster and superlattice geometries.
Confined dynamics of grafted polymer chains in solutions of linear polymer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poling-Skutvik, Ryan D.; Olafson, Katy N.; Narayanan, Suresh

Here, we measure the dynamics of high molecular weight polystyrene grafted to silica nanoparticles dispersed in semidilute solutions of linear polymer. Structurally, the linear free chains do not penetrate the grafted corona but increase the osmotic pressure of the solution, collapsing the grafted polymer and leading to eventual aggregation of the grafted particles at high matrix concentrations. Dynamically, the relaxations of the grafted polymer are controlled by the solvent viscosity according to the Zimm model on short time scales. On longer time scales, the grafted chains are confined by neighboring grafted chains, preventing full relaxation over the experimental time scale.more » Adding free linear polymer to the solution does not affect the initial Zimm relaxations of the grafted polymer but does increase the confinement of the grafted chains. Finally, our results elucidate the physics underlying the slow relaxations of grafted polymer.« less
Molecular biomimetics: GEPI-based biological routes to technology.

PubMed

Tamerler, Candan; Khatayevich, Dmitriy; Gungormus, Mustafa; Kacar, Turgay; Oren, E Emre; Hnilova, Marketa; Sarikaya, Mehmet

2010-01-01

In nature, the viability of biological systems is sustained via specific interactions among the tens of thousands of proteins, the major building blocks of organisms from the simplest single-celled to the most complex multicellular species. Biomolecule-material interaction is accomplished with molecular specificity and efficiency leading to the formation of controlled structures and functions at all scales of dimensional hierarchy. Through evolution, Mother Nature developed molecular recognition by successive cycles of mutation and selection. Molecular specificity of probe-target interactions, e.g., ligand-receptor, antigen-antibody, is always based on specific peptide molecular recognition. Using biology as a guide, we can now understand, engineer, and control peptide-material interactions and exploit them as a new design tool for novel materials and systems. We adapted the protocols of combinatorially designed peptide libraries, via both cell surface or phage display methods; using these we select short peptides with specificity to a variety of practical materials. These genetically engineered peptides for inorganics (GEPI) are then studied experimentally to establish their binding kinetics and surface stability. The bound peptide structure and conformations are interrogated both experimentally and via modeling, and self-assembly characteristics are tested via atomic force microscopy. We further engineer the peptide binding and assembly characteristics using a computational biomimetics approach where bioinformatics based peptide-sequence similarity analysis is developed to design higher generation function-specific peptides. The molecular biomimetic approach opens up new avenues for the design and utilization of multifunctional molecular systems in a wide-range of applications from tissue engineering, disease diagnostics, and therapeutics to various areas of nanotechnology where integration is required among inorganic, organic and biological materials. Here, we describe lessons from biology with examples of protein-mediated functional biological materials, explain how novel peptides can be designed with specific affinity to inorganic solids using evolutionary engineering approaches, give examples of their potential utilizations in technology and medicine, and, finally, provide a summary of challenges and future prospects. (c) 2010 Wiley Periodicals, Inc.
Weak competing interactions control assembly of strongly bonded TCNQ ionic acceptor molecules on silver surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Changwon; Rojas, Geoffrey A.; Jeon, Seokmin

2014-09-19

The energy scales of interactions that control molecular adsorption and assembly on surfaces can vary by several orders of magnitude, yet the importance of each contributing interaction is not apparent a priori. Tetracyanoquinodimethane (TCNQ) is an archetypal electron acceptor molecule and it is a key component of organic metals. On metal surfaces, this molecule also acts as an electron acceptor, producing negatively charged adsorbates. It is therefore rather intriguing to observe attractive molecular interactions in this system that were reported previously for copper and silver surfaces. In this paper, our experiments compared TCNQ adsorption on noble metal surfaces of Ag(100)more » and Ag(111). In both cases we found net attractive interactions down to the lowest coverage. However, the morphology of the assemblies was strikingly different, with two-dimensional islands on Ag(100) and one-dimensional chains on Ag(111) surfaces. This observation suggests that the registry effect governed by the molecular interaction with the underlying lattice potential is critical in determining the dimensionality of the molecular assembly. Using first-principles density functional calculations with a van der Waals correction scheme, we revealed that the strengths of major interactions (i.e., lattice potential corrugation, intermolecular attraction, and charge-transfer-induced repulsion) are all similar in energy. The van der Waals interactions, in particular, almost double the strength of attractive interactions, making the intermolecular potential comparable in strength to the diffusion potential and promoting self-assembly. However, it is the anisotropy of local intermolecular interactions that is primarily responsible for the difference in the topology of the molecular islands on Ag(100) and Ag(111) surfaces. Finally, we anticipate that the intermolecular potential will become more attractive and dominant over the diffusion potential with increasing molecular size, providing new design strategies for the structure and charge transfer within molecular layers.« less
Resolving the substructure of molecular clouds in the LMC

NASA Astrophysics Data System (ADS)

Wong, Tony; Hughes, Annie; Tokuda, Kazuki; Indebetouw, Remy; Wojciechowski, Evan; Bandurski, Jeffrey; MC3 Collaboration

2018-01-01

We present recent wide-field CO and 13CO mapping of giant molecular clouds in the Large Magellanic Cloud with ALMA. Our sample exhibits diverse star-formation properties, and reveals comparably diverse molecular cloud properties including surface density and velocity dispersion at a given scale. We first present the results of a recent study comparing two GMCs at the extreme ends of the star formation activity spectrum. Our quiescent cloud exhibits 10 times lower surface density and 5 times lower velocity dispersion than the active 30 Doradus cloud, yet in both clouds we find a wide range of line widths at the smallest resolved scales, spanning nearly the full range of line widths seen at all scales. This suggests an important role for feedback on sub-parsec scales, while the energetics on larger scales are dominated by clump-to-clump relative velocities. We then extend our analysis to four additional clouds that exhibit intermediate levels of star formation activity.

Coarse gaining of molecular crystals: limitations imposed by molecular flexibility

NASA Astrophysics Data System (ADS)

Picu, Catalin; Pal, Anirban

Molecular crystals include molecular electronics, energetic materials, pharmaceuticals and some food components. In many of these applications the small scale mechanical behavior of the crystal is important such as for example in energetic materials where detonation is induced by the formation of hot spots which are induced thermomechanically, and in pharmaceuticals where phase stability is critical for the biochemical activity of the drug. Accurate modeling of these processes requires resolving the atomistic scale details of the material. However, the cost of these models is very large due to the complexity of the molecules forming the crystal, and some form of coarse graning is necessary. In this study we identify the limitations imposed by the need to accurately capture molecular flexibility on the development of coarse grained models for the energetic molecular crystal RDX. We define guidelines for the definition of coarse grained models that target elastic and plastic crystal scale properties such as elastic constants, thermal expansion, compressibility, the critical stress for the motion of dislocations (Peierls stress) and the stacking fault energy This work was supported by the ARO through Grant W911NF-09-1-0330 and AFRL through Grant FA8651-16-1-0004.
Quantitative Resistance: More Than Just Perception of a Pathogen

PubMed Central

2017-01-01

Molecular plant pathology has focused on studying large-effect qualitative resistance loci that predominantly function in detecting pathogens and/or transmitting signals resulting from pathogen detection. By contrast, less is known about quantitative resistance loci, particularly the molecular mechanisms controlling variation in quantitative resistance. Recent studies have provided insight into these mechanisms, showing that genetic variation at hundreds of causal genes may underpin quantitative resistance. Loci controlling quantitative resistance contain some of the same causal genes that mediate qualitative resistance, but the predominant mechanisms of quantitative resistance extend beyond pathogen recognition. Indeed, most causal genes for quantitative resistance encode specific defense-related outputs such as strengthening of the cell wall or defense compound biosynthesis. Extending previous work on qualitative resistance to focus on the mechanisms of quantitative resistance, such as the link between perception of microbe-associated molecular patterns and growth, has shown that the mechanisms underlying these defense outputs are also highly polygenic. Studies that include genetic variation in the pathogen have begun to highlight a potential need to rethink how the field considers broad-spectrum resistance and how it is affected by genetic variation within pathogen species and between pathogen species. These studies are broadening our understanding of quantitative resistance and highlighting the potentially vast scale of the genetic basis of quantitative resistance. PMID:28302676
Duration of an intense laser pulse can determine the breakage of multiple chemical bonds

PubMed Central

Xie, Xinhua; Lötstedt, Erik; Roither, Stefan; Schöffler, Markus; Kartashov, Daniil; Midorikawa, Katsumi; Baltuška, Andrius; Yamanouchi, Kaoru; Kitzler, Markus

2015-01-01

Control over the breakage of a certain chemical bond in a molecule by an ultrashort laser pulse has been considered for decades. With the availability of intense non-resonant laser fields it became possible to pre-determine femtosecond to picosecond molecular bond breakage dynamics by controlled distortions of the electronic molecular system on sub-femtosecond time scales using field-sensitive processes such as strong-field ionization or excitation. So far, all successful demonstrations in this area considered only fragmentation reactions, where only one bond is broken and the molecule is split into merely two moieties. Here, using ethylene (C2H4) as an example, we experimentally investigate whether complex fragmentation reactions that involve the breakage of more than one chemical bond can be influenced by parameters of an ultrashort intense laser pulse. We show that the dynamics of removing three electrons by strong-field ionization determines the ratio of fragmentation of the molecular trication into two respectively three moieties. We observe a relative increase of two-body fragmentations with the laser pulse duration by almost an order of magnitude. Supported by quantum chemical simulations we explain our experimental results by the interplay between the dynamics of electron removal and nuclear motion. PMID:26271602
Chemically induced phospholipid translocation across biological membranes.

PubMed

Gurtovenko, Andrey A; Onike, Olajide I; Anwar, Jamshed

2008-09-02

Chemical means of manipulating the distribution of lipids across biological membranes is of considerable interest for many biomedical applications as a characteristic lipid distribution is vital for numerous cellular functions. Here we employ atomic-scale molecular simulations to shed light on the ability of certain amphiphilic compounds to promote lipid translocation (flip-flops) across membranes. We show that chemically induced lipid flip-flops are most likely pore-mediated: the actual flip-flop event is a very fast process (time scales of tens of nanoseconds) once a transient water defect has been induced by the amphiphilic chemical (dimethylsulfoxide in this instance). Our findings are consistent with available experimental observations and further emphasize the importance of transient membrane defects for chemical control of lipid distribution across cell membranes.
Universal scaling relations in scale-free structure formation

NASA Astrophysics Data System (ADS)

Guszejnov, Dávid; Hopkins, Philip F.; Grudić, Michael Y.

2018-07-01

A large number of astronomical phenomena exhibit remarkably similar scaling relations. The most well-known of these is the mass distribution dN/dM ∝ M-2 which (to first order) describes stars, protostellar cores, clumps, giant molecular clouds, star clusters, and even dark matter haloes. In this paper we propose that this ubiquity is not a coincidence and that it is the generic result of scale-free structure formation where the different scales are uncorrelated. We show that all such systems produce a mass function proportional to M-2 and a column density distribution with a power-law tail of dA/dln Σ ∝ Σ-1. In the case where structure formation is controlled by gravity the two-point correlation becomes ξ2D ∝ R-1. Furthermore, structures formed by such processes (e.g. young star clusters, DM haloes) tend to a ρ ∝ R-3 density profile. We compare these predictions with observations, analytical fragmentation cascade models, semi-analytical models of gravito-turbulent fragmentation, and detailed `full physics' hydrodynamical simulations. We find that these power laws are good first-order descriptions in all cases.
Universal Scaling Relations in Scale-Free Structure Formation

NASA Astrophysics Data System (ADS)

Guszejnov, Dávid; Hopkins, Philip F.; Grudić, Michael Y.

2018-04-01

A large number of astronomical phenomena exhibit remarkably similar scaling relations. The most well-known of these is the mass distribution dN/dM∝M-2 which (to first order) describes stars, protostellar cores, clumps, giant molecular clouds, star clusters and even dark matter halos. In this paper we propose that this ubiquity is not a coincidence and that it is the generic result of scale-free structure formation where the different scales are uncorrelated. We show that all such systems produce a mass function proportional to M-2 and a column density distribution with a power law tail of dA/d lnΣ∝Σ-1. In the case where structure formation is controlled by gravity the two-point correlation becomes ξ2D∝R-1. Furthermore, structures formed by such processes (e.g. young star clusters, DM halos) tend to a ρ∝R-3 density profile. We compare these predictions with observations, analytical fragmentation cascade models, semi-analytical models of gravito-turbulent fragmentation and detailed "full physics" hydrodynamical simulations. We find that these power-laws are good first order descriptions in all cases.
An Affective Neuroscience Framework for the Molecular Study of Internet Addiction.

PubMed

Montag, Christian; Sindermann, Cornelia; Becker, Benjamin; Panksepp, Jaak

2016-01-01

Internet addiction represents an emerging global health issue. Increasing efforts have been made to characterize risk factors for the development of Internet addiction and consequences of excessive Internet use. During the last years, classic research approaches from psychology considering personality variables as vulnerability factor, especially in conjunction with neuroscience approaches such as brain imaging, have led to coherent theoretical conceptualizations of Internet addiction. Although such conceptualizations can be valuable aid, the research field is currently lacking a comprehensive framework for determining brain-based and neurochemical markers of Internet addiction. The present work aims at providing a framework on the molecular level as a basis for future research on the neural and behavioral level, in order to facilitate a comprehensive neurobiological model of Internet addiction and its clinical symptomatology. To help establish such a molecular framework for the study of Internet addiction, we investigated in N = 680 participants associations between individual differences in tendencies toward Internet addiction measured by the Generalized Problematic Internet Use Scale-2 (GPIUS-2) and individual differences in primary emotional systems as assessed by the Affective Neuroscience Personality Scales (ANPS). Regression analysis revealed that the ANPS scales FEAR and SADNESS were the ANPS scales most robustly positively linked to several (sub)scales of the GPIUS-2. Also the scales SEEKING, CARE and PLAY explain variance in some of the GPIUS-2 subscales. As such, these scales are negatively linked to the GPIUS-2 subscales. As the ANPS has been constructed on substantial available brain data including an extensive molecular body with respect to evolutionary highly conserved emotional circuitry in the ancient mammalian brain, the present study gives first ideas on putative molecular mechanisms underlying different facets of Internet addiction as derived from associations between tendencies toward Internet addiction and individual differences in primary emotional systems. For example, as SADNESS is linked to the overall GPIUS-2 score, and the neuropeptide oxytocin is known to downregulate SADNESS, it is conceivable that the neuropeptide might play a role in Internet addition on the molecular level. Our findings provide a theoretical framework potentially illuminating the molecular underpinnings of Internet addiction. Finally, we also present data on the ANPS and smartphone addiction at the end of the paper. Similar to the reported associations between the ANPS and the GPIUS-2, these correlations might provide an initial outline for a framework guiding future studies that aim to address the molecular basis of smartphone addiction.
An Affective Neuroscience Framework for the Molecular Study of Internet Addiction

PubMed Central

Montag, Christian; Sindermann, Cornelia; Becker, Benjamin; Panksepp, Jaak

2016-01-01

Internet addiction represents an emerging global health issue. Increasing efforts have been made to characterize risk factors for the development of Internet addiction and consequences of excessive Internet use. During the last years, classic research approaches from psychology considering personality variables as vulnerability factor, especially in conjunction with neuroscience approaches such as brain imaging, have led to coherent theoretical conceptualizations of Internet addiction. Although such conceptualizations can be valuable aid, the research field is currently lacking a comprehensive framework for determining brain-based and neurochemical markers of Internet addiction. The present work aims at providing a framework on the molecular level as a basis for future research on the neural and behavioral level, in order to facilitate a comprehensive neurobiological model of Internet addiction and its clinical symptomatology. To help establish such a molecular framework for the study of Internet addiction, we investigated in N = 680 participants associations between individual differences in tendencies toward Internet addiction measured by the Generalized Problematic Internet Use Scale-2 (GPIUS-2) and individual differences in primary emotional systems as assessed by the Affective Neuroscience Personality Scales (ANPS). Regression analysis revealed that the ANPS scales FEAR and SADNESS were the ANPS scales most robustly positively linked to several (sub)scales of the GPIUS-2. Also the scales SEEKING, CARE and PLAY explain variance in some of the GPIUS-2 subscales. As such, these scales are negatively linked to the GPIUS-2 subscales. As the ANPS has been constructed on substantial available brain data including an extensive molecular body with respect to evolutionary highly conserved emotional circuitry in the ancient mammalian brain, the present study gives first ideas on putative molecular mechanisms underlying different facets of Internet addiction as derived from associations between tendencies toward Internet addiction and individual differences in primary emotional systems. For example, as SADNESS is linked to the overall GPIUS-2 score, and the neuropeptide oxytocin is known to downregulate SADNESS, it is conceivable that the neuropeptide might play a role in Internet addition on the molecular level. Our findings provide a theoretical framework potentially illuminating the molecular underpinnings of Internet addiction. Finally, we also present data on the ANPS and smartphone addiction at the end of the paper. Similar to the reported associations between the ANPS and the GPIUS-2, these correlations might provide an initial outline for a framework guiding future studies that aim to address the molecular basis of smartphone addiction. PMID:28018255
Peridynamic Multiscale Finite Element Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Costa, Timothy; Bond, Stephen D.; Littlewood, David John

The problem of computing quantum-accurate design-scale solutions to mechanics problems is rich with applications and serves as the background to modern multiscale science research. The prob- lem can be broken into component problems comprised of communicating across adjacent scales, which when strung together create a pipeline for information to travel from quantum scales to design scales. Traditionally, this involves connections between a) quantum electronic structure calculations and molecular dynamics and between b) molecular dynamics and local partial differ- ential equation models at the design scale. The second step, b), is particularly challenging since the appropriate scales of molecular dynamic andmore » local partial differential equation models do not overlap. The peridynamic model for continuum mechanics provides an advantage in this endeavor, as the basic equations of peridynamics are valid at a wide range of scales limiting from the classical partial differential equation models valid at the design scale to the scale of molecular dynamics. In this work we focus on the development of multiscale finite element methods for the peridynamic model, in an effort to create a mathematically consistent channel for microscale information to travel from the upper limits of the molecular dynamics scale to the design scale. In particular, we first develop a Nonlocal Multiscale Finite Element Method which solves the peridynamic model at multiple scales to include microscale information at the coarse-scale. We then consider a method that solves a fine-scale peridynamic model to build element-support basis functions for a coarse- scale local partial differential equation model, called the Mixed Locality Multiscale Finite Element Method. Given decades of research and development into finite element codes for the local partial differential equation models of continuum mechanics there is a strong desire to couple local and nonlocal models to leverage the speed and state of the art of local models with the flexibility and accuracy of the nonlocal peridynamic model. In the mixed locality method this coupling occurs across scales, so that the nonlocal model can be used to communicate material heterogeneity at scales inappropriate to local partial differential equation models. Additionally, the computational burden of the weak form of the peridynamic model is reduced dramatically by only requiring that the model be solved on local patches of the simulation domain which may be computed in parallel, taking advantage of the heterogeneous nature of next generation computing platforms. Addition- ally, we present a novel Galerkin framework, the 'Ambulant Galerkin Method', which represents a first step towards a unified mathematical analysis of local and nonlocal multiscale finite element methods, and whose future extension will allow the analysis of multiscale finite element methods that mix models across scales under certain assumptions of the consistency of those models.« less
EDITORIAL: Design and function of molecular and bioelectronics devices

NASA Astrophysics Data System (ADS)

Krstic, Predrag; Forzani, Erica; Tao, Nongjian; Korkin, Anatoli

2007-10-01

Further rapid progress of electronics, in particular the increase of computer power and breakthroughs in sensor technology for industrial, medical diagnostics and environmental applications, strongly depends on the scaling of electronic devices, ultimately to the size of molecules. Design of controllable molecular-scale devices may resolve the problem of energy dissipation at the nanoscale and take advantage of molecular self-assembly in the so-called bottom-up approach. This special issue of Nanotechnology is devoted to a better understanding of the function and design of molecular-scale devices that are relevant to future electronics and sensor technology. Papers contained in this special issue are selected from the symposium Nano and Giga Challenges in Electronics and Photonics: From Atoms to Materials to Devices to System Architecture (12-16 March, 2007, Phoenix, Arizona, USA), as well as from original and novel scientific contributions of invited world-renown researchers. It addresses both theoretical and experimental achievements in the fields of molecular and bioelectronics, chemical and biosensors at the molecular level, including carbon nanotubes, novel nanostructures, as well as related research areas and industrial applications. The conference series Nano and Giga Challenges in Electronics and Photonics was launched as a truly interdisciplinary forum to bridge scientists and engineers to work across boundaries in the design of future information technologies, from atoms to materials to devices to system architecture. Following the first two successful meetings in Moscow, Russia (NGCM2002) and Krakow, Poland (NGCM2004), the third Nano and Giga Forum (NGC2007) was held in 2007 hosted by Arizona State University. Besides this special issue of Nanotechnology, two other collections (in the journal Solid State Electronics and the tutorial book in the series Nanostructure Science and Technology Springer) have published additional selected and invited papers from NGC2007. The NGC2007 meeting, which included two days of tutorials (Spring School) and a three day symposium, attracted approximately 400 participants from academic, industrial and governmental research institutions from 41 countries, and covered recent developments in the fabrication and functionality of nano-scale materials, devices and system architecture from advanced CMOS to molecular electronics, photonics, optoelectronics and magnetic materials and devices. The success of the conference would not have been possible without generous support from many sponsors and research institutions, especially from Arizona State University (conference host and co-organizer), International Science and Technology Center (ISTC), National Science Foundation (NSFT), Defense Advanced Research Agency (DARPA), Office of Naval Research, Army Research Office, Computational Chemistry List (CCL), Springer Publisher, City of Tempe, STMicroelectronics, Quarles & Brady LLP, Oak Ridge National Laboratory, Canadian Consulate in Phoenix, Salt River Project (SRP) and many other local, national and international and individual supporters. We would like to acknowledge the shared responsibility for this special issue of Nanotechnology on molecular and bioelectronics, and the highly professional support from Dr Nina Couzin, Dr Alex Wotherspoon and the Nanotechnology team from the IOP Publishing. We also acknowledge the exception made in allowing the publication of some material that is outside the normal scope of Nanotechnology.
Design and function of molecular and bioelectronics devices.

PubMed

Krstic, Predrag; Forzani, Erica; Tao, Nongjian; Korkin, Anatoli

2007-10-24

Further rapid progress of electronics, in particular the increase of computer power and breakthroughs in sensor technology for industrial, medical diagnostics and environmental applications, strongly depends on the scaling of electronic devices, ultimately to the size of molecules. Design of controllable molecular-scale devices may resolve the problem of energy dissipation at the nanoscale and take advantage of molecular self-assembly in the so-called bottom-up approach. This special issue of Nanotechnology is devoted to a better understanding of the function and design of molecular-scale devices that are relevant to future electronics and sensor technology. Papers contained in this special issue are selected from the symposium Nano and Giga Challenges in Electronics and Photonics: From Atoms to Materials to Devices to System Architecture (12-16 March, 2007, Phoenix, Arizona, USA), as well as from original and novel scientific contributions of invited world-renown researchers. It addresses both theoretical and experimental achievements in the fields of molecular and bioelectronics, chemical and biosensors at the molecular level, including carbon nanotubes, novel nanostructures, as well as related research areas and industrial applications. The conference series Nano and Giga Challenges in Electronics and Photonics was launched as a truly interdisciplinary forum to bridge scientists and engineers to work across boundaries in the design of future information technologies, from atoms to materials to devices to system architecture. Following the first two successful meetings in Moscow, Russia (NGCM2002) and Krakow, Poland (NGCM2004), the third Nano and Giga Forum (NGC2007) was held in 2007 hosted by Arizona State University. Besides this special issue of Nanotechnology, two other collections (in the journal Solid State Electronics and the tutorial book in the series Nanostructure Science and Technology Springer) have published additional selected and invited papers from NGC2007. The NGC2007 meeting, which included two days of tutorials (Spring School) and a three day symposium, attracted approximately 400 participants from academic, industrial and governmental research institutions from 41 countries, and covered recent developments in the fabrication and functionality of nano-scale materials, devices and system architecture from advanced CMOS to molecular electronics, photonics, optoelectronics and magnetic materials and devices. The success of the conference would not have been possible without generous support from many sponsors and research institutions, especially from Arizona State University (conference host and co-organizer), International Science and Technology Center (ISTC), National Science Foundation (NSFT), Defense Advanced Research Agency (DARPA), Office of Naval Research, Army Research Office, Computational Chemistry List (CCL), Springer Publisher, City of Tempe, STMicroelectronics, Quarles & Brady LLP, Oak Ridge National Laboratory, Canadian Consulate in Phoenix, Salt River Project (SRP) and many other local, national and international and individual supporters. We would like to acknowledge the shared responsibility for this special issue of Nanotechnology on molecular and bioelectronics, and the highly professional support from Dr Nina Couzin, Dr Alex Wotherspoon and the Nanotechnology team from the IOP Publishing. We also acknowledge the exception made in allowing the publication of some material that is outside the normal scope of Nanotechnology.
On the physical mechanisms governing the cloud lifecycle in the Central Molecular Zone of the Milky Way

NASA Astrophysics Data System (ADS)

Jeffreson, S. M. R.; Kruijssen, J. M. D.; Krumholz, M. R.; Longmore, S. N.

2018-05-01

We apply an analytic theory for environmentally-dependent molecular cloud lifetimes to the Central Molecular Zone of the Milky Way. Within this theory, the cloud lifetime in the Galactic centre is obtained by combining the time-scales for gravitational instability, galactic shear, epicyclic perturbations and cloud-cloud collisions. We find that at galactocentric radii ˜45-120 pc, corresponding to the location of the `100-pc stream', cloud evolution is primarily dominated by gravitational collapse, with median cloud lifetimes between 1.4 and 3.9 Myr. At all other galactocentric radii, galactic shear dominates the cloud lifecycle, and we predict that molecular clouds are dispersed on time-scales between 3 and 9 Myr, without a significant degree of star formation. Along the outer edge of the 100-pc stream, between radii of 100 and 120 pc, the time-scales for epicyclic perturbations and gravitational free-fall are similar. This similarity of time-scales lends support to the hypothesis that, depending on the orbital geometry and timing of the orbital phase, cloud collapse and star formation in the 100-pc stream may be triggered by a tidal compression at pericentre. Based on the derived time-scales, this should happen in approximately 20 per cent of all accretion events onto the 100-pc stream.
Discrepancy between species borders at morphological and molecular levels in the genus Cochliopodium (Amoebozoa, Himatismenida), with the description of Cochliopodium plurinucleolum n. sp.

PubMed

Geisen, Stefan; Kudryavtsev, Alexander; Bonkowski, Michael; Smirnov, Alexey

2014-05-01

Amoebae of the genus Cochliopodium are characterized by a tectum that is a layer of scales covering the dorsal surface of the cell. A combination of scale structure, morphological features and, nowadays, molecular information allows species discrimination. Here we describe a soil species Cochliopodium plurinucleolum n. sp. that besides strong genetic divergence from all currently described species of Cochliopodium differs morphologically by the presence of several peripheral nucleoli in the nucleus. Further, we unambiguously show that the Golgi attachment associated with a dictyosome in Cochliopodium is a cytoplasmic microtubule organizing center (MTOC). Last, we provide detailed morphological and molecular information on the sister clade of C. plurinucleolum, containing C. minus, C. minutoidum, C. pentatrifurcatum and C. megatetrastylus. These species share nearly identical sequences of both, small subunit ribosomal RNA and partial Cox1 genes, and nearly identical structure of the scales. Scales of C. pentatrifurcatum differ, however, strongly from scales of the others while sequences of C. pentatrifurcatum and C. minus are nearly identical. These discrepancies urge for future sampling efforts to disentangle species characteristics within Cochliopdium and to investigate morphological and molecular patterns that allow reliable species differentiation. Copyright © 2014 Elsevier GmbH. All rights reserved.
Self-Healing Composite of Thermoset Polymer and Programmed Super Contraction Fibers

NASA Technical Reports Server (NTRS)

Li, Guoqiang (Inventor); Meng, Harper (Inventor)

2016-01-01

A composition comprising thermoset polymer, shape memory polymer to facilitate macro scale damage closure, and a thermoplastic polymer for molecular scale healing is disclosed; the composition has the ability to resolve structural defects by a bio-mimetic close-then heal process. In use, the shape memory polymer serves to bring surfaces of a structural defect into approximation, whereafter use of the thermoplastic polymer for molecular scale healing allowed for movement of the thermoplastic polymer into the defect and thus obtain molecular scale healing. The thermoplastic can be fibers, particles or spheres which are used by heating to a level at or above the thermoplastic's melting point, then cooling of the composition below the melting temperature of the thermoplastic. Compositions of the invention have the ability to not only close macroscopic defects, but also to do so repeatedly even if another wound/damage occurs in a previously healed/repaired area.
Combinatorial screening of halide perovskite thin films and solar cells by mask-defined IR laser molecular beam epitaxy

PubMed Central

Kawashima, Kazuhiro; Okamoto, Yuji; Annayev, Orazmuhammet; Toyokura, Nobuo; Takahashi, Ryota; Lippmaa, Mikk; Itaka, Kenji; Suzuki, Yoshikazu; Matsuki, Nobuyuki; Koinuma, Hideomi

2017-01-01

Abstract As an extension of combinatorial molecular layer epitaxy via ablation of perovskite oxides by a pulsed excimer laser, we have developed a laser molecular beam epitaxy (MBE) system for parallel integration of nano-scaled thin films of organic–inorganic hybrid materials. A pulsed infrared (IR) semiconductor laser was adopted for thermal evaporation of organic halide (A-site: CH3NH3I) and inorganic halide (B-site: PbI2) powder targets to deposit repeated A/B bilayer films where the thickness of each layer was controlled on molecular layer scale by programming the evaporation IR laser pulse number, length, or power. The layer thickness was monitored with an in situ quartz crystal microbalance and calibrated against ex situ stylus profilometer measurements. A computer-controlled movable mask system enabled the deposition of combinatorial thin film libraries, where each library contains a vertically homogeneous film with spatially programmable A- and B-layer thicknesses. On the composition gradient film, a hole transport Spiro-OMeTAD layer was spin-coated and dried followed by the vacuum evaporation of Ag electrodes to form the solar cell. The preliminary cell performance was evaluated by measuring I-V characteristics at seven different positions on the 12.5 mm × 12.5 mm combinatorial library sample with seven 2 mm × 4 mm slits under a solar simulator irradiation. The combinatorial solar cell library clearly demonstrated that the energy conversion efficiency sharply changes from nearly zero to 10.2% as a function of the illumination area in the library. The exploration of deposition parameters for obtaining optimum performance could thus be greatly accelerated. Since the thickness ratio of PbI2 and CH3NH3I can be freely chosen along the shadow mask movement, these experiments show the potential of this system for high-throughput screening of optimum chemical composition in the binary film library and application to halide perovskite solar cell. PMID:28567176
Quantum Nuclear Dynamics Pumped and Probed by Ultrafast Polarization Controlled Steering of a Coherent Electronic State in LiH.

PubMed

Nikodem, Astrid; Levine, R D; Remacle, F

2016-05-19

The quantum wave packet dynamics following a coherent electronic excitation of LiH by an ultrashort, polarized, strong one-cycle infrared optical pulse is computed on several electronic states using a grid method. The coupling to the strong field of the pump and the probe pulses is included in the Hamiltonian used to solve the time-dependent Schrodinger equation. The polarization of the pump pulse allows us to control the localization in time and in space of the nonequilibrium coherent electronic motion and the subsequent nuclear dynamics. We show that transient absorption, resulting from the interaction of the total molecular dipole with the electric fields of the pump and the probe, is a very versatile probe of the different time scales of the vibronic dynamics. It allows probing both the ultrashort, femtosecond time scale of the electronic coherences as well as the longer dozens of femtoseconds time scales of the nuclear motion on the excited electronic states. The ultrafast beatings of the electronic coherences in space and in time are shown to be modulated by the different periods of the nuclear motion.
Systems Biophysics of Gene Expression

PubMed Central

Vilar, Jose M.G.; Saiz, Leonor

2013-01-01

Gene expression is a process central to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular and extracellular changes. This diversity in scales poses fundamental challenges to the use of traditional approaches to fully understand even the simplest gene expression systems. Recent advances in computational systems biophysics have provided promising avenues to reliably integrate the molecular detail of biophysical process into the system behavior. Here, we review recent advances in the description of gene regulation as a system of biophysical processes that extend from specific protein-DNA interactions to the combinatorial assembly of nucleoprotein complexes. There is now basic mechanistic understanding on how promoters controlled by multiple, local and distal, DNA binding sites for transcription factors can actively control transcriptional noise, cell-to-cell variability, and other properties of gene regulation, including precision and flexibility of the transcriptional responses. PMID:23790365
Deep eutectic-solvothermal synthesis of nanostructured ceria

PubMed Central

Hammond, Oliver S.; Edler, Karen J.; Bowron, Daniel T.; Torrente-Murciano, Laura

2017-01-01

Ceria is a technologically important material with applications in catalysis, emissions control and solid-oxide fuel cells. Nanostructured ceria becomes profoundly more active due to its enhanced surface area to volume ratio, reactive surface oxygen vacancy concentration and superior oxygen storage capacity. Here we report the synthesis of nanostructured ceria using the green Deep Eutectic Solvent reline, which allows morphology and porosity control in one of the less energy-intensive routes reported to date. Using wide Q-range liquid-phase neutron diffraction, we elucidate the mechanism of reaction at a molecular scale at considerably milder conditions than the conventional hydrothermal synthetic routes. The reline solvent plays the role of a latent supramolecular catalyst where the increase in reaction rate from solvent-driven pre-organization of the reactants is most significant. This fundamental understanding of deep eutectic-solvothermal methodology will enable future developments in low-temperature synthesis of nanostructured ceria, facilitating its large-scale manufacturing using green, economic, non-toxic solvents. PMID:28120829
Electrically modulated capillary filling imbibition of nematic liquid crystals

NASA Astrophysics Data System (ADS)

Dhar, Jayabrata; Chakraborty, Suman

2018-04-01

The flow of nematic liquid crystals (NLCs) in the presence of an electric field is typically characterized by the variation in its rheological properties due to transition in its molecular arrangements. Here, we bring out a nontrivial interplay of a consequent alteration in the resistive viscous effects and driving electrocapillary interactions, toward maneuvering the capillary filling dynamics over miniaturized scales. Considering a dynamic interplay of the relevant bulk and interfacial forces acting in tandem, our results converge nicely to previously reported experimental data. Finally, we attempt a scaling analysis to bring forth further insight to the reported observations. Our analysis paves the way for the development of microfluidic strategies with previously unexplored paradigms of interaction between electrical and fluidic phenomenon, providing with an augmented controllability on capillary filling as compared to tthose reported to be achievable by the existing strategies. This, in turn, holds utilitarian scopes in improved designs of functional capillarities in electro-optical systems, electrorheological utilities, electrokinetic flow control, as well as in interfacing and imaging systems for biomedical microdevices.
Knowledge environments representing molecular entities for the virtual physiological human.

PubMed

Hofmann-Apitius, Martin; Fluck, Juliane; Furlong, Laura; Fornes, Oriol; Kolárik, Corinna; Hanser, Susanne; Boeker, Martin; Schulz, Stefan; Sanz, Ferran; Klinger, Roman; Mevissen, Theo; Gattermayer, Tobias; Oliva, Baldo; Friedrich, Christoph M

2008-09-13

In essence, the virtual physiological human (VPH) is a multiscale representation of human physiology spanning from the molecular level via cellular processes and multicellular organization of tissues to complex organ function. The different scales of the VPH deal with different entities, relationships and processes, and in consequence the models used to describe and simulate biological functions vary significantly. Here, we describe methods and strategies to generate knowledge environments representing molecular entities that can be used for modelling the molecular scale of the VPH. Our strategy to generate knowledge environments representing molecular entities is based on the combination of information extraction from scientific text and the integration of information from biomolecular databases. We introduce @neuLink, a first prototype of an automatically generated, disease-specific knowledge environment combining biomolecular, chemical, genetic and medical information. Finally, we provide a perspective for the future implementation and use of knowledge environments representing molecular entities for the VPH.

Spiers Memorial Lecture. Molecular mechanics and molecular electronics.

PubMed

Beckman, Robert; Beverly, Kris; Boukai, Akram; Bunimovich, Yuri; Choi, Jang Wook; DeIonno, Erica; Green, Johnny; Johnston-Halperin, Ezekiel; Luo, Yi; Sheriff, Bonnie; Stoddart, Fraser; Heath, James R

2006-01-01

We describe our research into building integrated molecular electronics circuitry for a diverse set of functions, and with a focus on the fundamental scientific issues that surround this project. In particular, we discuss experiments aimed at understanding the function of bistable rotaxane molecular electronic switches by correlating the switching kinetics and ground state thermodynamic properties of those switches in various environments, ranging from the solution phase to a Langmuir monolayer of the switching molecules sandwiched between two electrodes. We discuss various devices, low bit-density memory circuits, and ultra-high density memory circuits that utilize the electrochemical switching characteristics of these molecules in conjunction with novel patterning methods. We also discuss interconnect schemes that are capable of bridging the micrometre to submicrometre length scales of conventional patterning approaches to the near-molecular length scales of the ultra-dense memory circuits. Finally, we discuss some of the challenges associated with fabricated ultra-dense molecular electronic integrated circuits.
Multi-scale simulations of apatite-collagen composites: from molecules to materials

NASA Astrophysics Data System (ADS)

Zahn, Dirk

2017-03-01

We review scale-bridging simulation studies for the exploration of atomicto-meso scale processes that account for the unique structure and mechanic properties of apatite-protein composites. As the atomic structure and composition of such complex biocomposites only partially is known, the first part (i) of our modelling studies is dedicated to realistic crystal nucleation scenarios of inorganic-organic composites. Starting from the association of single ions, recent insights range from the mechanisms of motif formation, ripening reactions and the self-organization of nanocrystals, including their interplay with growth-controlling molecular moieties. On this basis, (ii) reliable building rules for unprejudiced scale-up models can be derived to model bulk materials. This is exemplified for (enamel-like) apatite-protein composites, encompassing up to 106 atom models to provide a realistic account of the 10 nm length scale, whilst model coarsening is used to reach μm length scales. On this basis, a series of deformation and fracture simulation studies were performed and helped to rationalize biocomposite hardness, plasticity, toughness, self-healing and fracture mechanisms. Complementing experimental work, these modelling studies provide particularly detailed insights into the relation of hierarchical composite structure and favorable mechanical properties.
Molecular cloud-scale star formation in NGC 300

DOE Office of Scientific and Technical Information (OSTI.GOV)

Faesi, Christopher M.; Lada, Charles J.; Forbrich, Jan

2014-07-01

We present the results of a galaxy-wide study of molecular gas and star formation in a sample of 76 H II regions in the nearby spiral galaxy NGC 300. We have measured the molecular gas at 250 pc scales using pointed CO(J = 2-1) observations with the Atacama Pathfinder Experiment telescope. We detect CO in 42 of our targets, deriving molecular gas masses ranging from our sensitivity limit of ∼10{sup 5} M {sub ☉} to 7 × 10{sup 5} M {sub ☉}. We find a clear decline in the CO detection rate with galactocentric distance, which we attribute primarily tomore » the decreasing radial metallicity gradient in NGC 300. We combine Galaxy Evolution Explorer far-ultraviolet, Spitzer 24 μm, and Hα narrowband imaging to measure the star formation activity in our sample. We have developed a new direct modeling approach for computing star formation rates (SFRs) that utilizes these data and population synthesis models to derive the masses and ages of the young stellar clusters associated with each of our H II region targets. We find a characteristic gas depletion time of 230 Myr at 250 pc scales in NGC 300, more similar to the results obtained for Milky Way giant molecular clouds than the longer (>2 Gyr) global depletion times derived for entire galaxies and kiloparsec-sized regions within them. This difference is partially due to the fact that our study accounts for only the gas and stars within the youngest star-forming regions. We also note a large scatter in the NGC 300 SFR-molecular gas mass scaling relation that is furthermore consistent with the Milky Way cloud results. This scatter likely represents real differences in giant molecular cloud physical properties such as the dense gas fraction.« less
Diagnosing schistosomiasis: where are we?

PubMed

Gomes, Luciana Inácia; Enk, Martin Johannes; Rabello, Ana

2014-01-01

In light of the World Health Organization's initiative to extend schistosomiasis morbidity and mortality control programs by including a disease elimination strategy in low endemic settings, this paper reviews diagnostic tools described during the last decades and provide an overview of ongoing efforts in making an efficient diagnostic tool available worldwide. A literature search on PubMed using the search criteria schistosomiasis and diagnosis within the period from 1978 to 2013 was carried out. Articles with abstract in English and that used laboratory techniques specifically developed for the detection of schistosomiasis in humans were included. Publications were categorized according to the methodology applied (parasitological, immunological, or molecular) and stage of development (in house development, limited field, or large scale field testing). The initial research generated 4,535 publications, of which only 643 met the inclusion criteria. The vast majority (537) of the publications focused on immunological techniques; 81 focused on parasitological diagnosis, and 25 focused on molecular diagnostic methods. Regarding the stage of development, 307 papers referred to in-house development, 202 referred to limited field tests, and 134 referred to large scale field testing. The data obtained show that promising new diagnostic tools, especially for Schistosoma antigen and deoxyribonucleic acid (DNA) detection, which are characterized by high sensitivity and specificity, are being developed. In combination with international funding initiatives these tools may result in a significant step forward in successful disease elimination and surveillance, which is to make efficient tests accessible and its large use self-sustainable for control programs in endemic countries.
An integrated, cross-disciplinary study of soil hydrophobicity at atomic, molecular, core and landscape scales

NASA Astrophysics Data System (ADS)

Matthews, G. Peter; Doerr, Stefan; Van Keulen, Geertje; Dudley, Ed; Francis, Lewis; Whalley, Richard; Gazze, Andrea; Hallin, Ingrid; Quinn, Gerry; Sinclair, Kat; Ashton, Rhys

2017-04-01

Soil hydrophobicity can lead to reduced soil fertility and heightened flood risk caused by increased run-off. Soil hydrophobicity is a well-known phenomenon when induced by natural events such as wildfires and anthropogenic causes including adding organic wastes or hydrocarbon contaminants. This presentation concerns a much more subtle effect - the naturally occurring changes between hydrophilic and hydrophobic states caused by periods of wetness and drought. Although subtle, they nevertheless affect vast areas of soil, and so their effects can be very significant, and are predicted to increase under climate change conditions. To understand the effect, a major interdisciplinary study has been commissioned by the UK's Natural Environment Research Council (NERC) to investigate soil hydrophobicity over length scales ranging from atomic through molecular, core and landscape scale. We present the key findings from the many publications currently in preparation. The programme is predicated on the hypothesis that changes in soil protein abundance and localization, induced by variations in soil moisture and temperature, are crucial driving forces for transitions between hydrophobic and hydrophilic conditions at soil particle surfaces, and that these effects can be meaningfully upscaled from molecular to landscape scale. Three soils were chosen based on the severity of hydrophobicity that can be achieved in the field: severe to extreme (natural rough pasture, Wales), intermediate to severe (pasture, Wales), and subcritical (managed research grassland, Rothamsted Research, England). The latter is already highly characterised so was also used as a control. Hydrophobic/ hydrophilic transitions were determined from water droplet penetration times. Scientific advances in the following five areas will be described: (i) the identification of these soil proteins by proteomic methods, using novel separation methods which reduces interference by humic acids, and allows identification by ESI and MALDI TOF mass spectrometry and database searches, (ii) the examination of such proteins, which form ordered hydrophobic ridges, and measurement of their elasticity, stickiness and hydrophobicity at nano- to microscale using atomic force microscopy adapted for the rough surfaces of soil particles, (iii) the novel use of a picoliter goniometer to show hydrophobic effects at a 1 micron diameter droplet level, which avoids the averaging over soil cores and particles evident in microliter goniometry, with which the results are compared, (iv) measurements at core scale using water retention and wicking experiments, and (v) the modelling and upscaling of the results from molecular to core scale using the PoreXpert void network model of dynamic wetting and Haines jumps. An explanation will also be given as to how the results will be further upscaled by incorporation into the JULES hydrological model of the UK Meteorological Office, used to predict flooding for different soil types and usage.
Conflicting Selection Pressures Will Constrain Viral Escape from Interfering Particles: Principles for Designing Resistance-Proof Antivirals.

PubMed

Rast, Luke I; Rouzine, Igor M; Rozhnova, Ganna; Bishop, Lisa; Weinberger, Ariel D; Weinberger, Leor S

2016-05-01

The rapid evolution of RNA-encoded viruses such as HIV presents a major barrier to infectious disease control using conventional pharmaceuticals and vaccines. Previously, it was proposed that defective interfering particles could be developed to indefinitely control the HIV/AIDS pandemic; in individual patients, these engineered molecular parasites were further predicted to be refractory to HIV's mutational escape (i.e., be 'resistance-proof'). However, an outstanding question has been whether these engineered interfering particles-termed Therapeutic Interfering Particles (TIPs)-would remain resistance-proof at the population-scale, where TIP-resistant HIV mutants may transmit more efficiently by reaching higher viral loads in the TIP-treated subpopulation. Here, we develop a multi-scale model to test whether TIPs will maintain indefinite control of HIV at the population-scale, as HIV ('unilaterally') evolves toward TIP resistance by limiting the production of viral proteins available for TIPs to parasitize. Model results capture the existence of two intrinsic evolutionary tradeoffs that collectively prevent the spread of TIP-resistant HIV mutants in a population. First, despite their increased transmission rates in TIP-treated sub-populations, unilateral TIP-resistant mutants are shown to have reduced transmission rates in TIP-untreated sub-populations. Second, these TIP-resistant mutants are shown to have reduced growth rates (i.e., replicative fitness) in both TIP-treated and TIP-untreated individuals. As a result of these tradeoffs, the model finds that TIP-susceptible HIV strains continually outcompete TIP-resistant HIV mutants at both patient and population scales when TIPs are engineered to express >3-fold more genomic RNA than HIV expresses. Thus, the results provide design constraints for engineering population-scale therapies that may be refractory to the acquisition of antiviral resistance.
Molecular dynamics simulations of large macromolecular complexes.

PubMed

Perilla, Juan R; Goh, Boon Chong; Cassidy, C Keith; Liu, Bo; Bernardi, Rafael C; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus

2015-04-01

Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone. Copyright © 2015 Elsevier Ltd. All rights reserved.
Simulating Energy Relaxation in Pump-Probe Vibrational Spectroscopy of Hydrogen-Bonded Liquids.

PubMed

Dettori, Riccardo; Ceriotti, Michele; Hunger, Johannes; Melis, Claudio; Colombo, Luciano; Donadio, Davide

2017-03-14

We introduce a nonequilibrium molecular dynamics simulation approach, based on the generalized Langevin equation, to study vibrational energy relaxation in pump-probe spectroscopy. A colored noise thermostat is used to selectively excite a set of vibrational modes, leaving the other modes nearly unperturbed, to mimic the effect of a monochromatic laser pump. Energy relaxation is probed by analyzing the evolution of the system after excitation in the microcanonical ensemble, thus providing direct information about the energy redistribution paths at the molecular level and their time scale. The method is applied to hydrogen-bonded molecular liquids, specifically deuterated methanol and water, providing a robust picture of energy relaxation at the molecular scale.
Coexistence of both gyroid chiralities in individual butterfly wing scales of Callophrys rubi

PubMed Central

Winter, Benjamin; Butz, Benjamin; Dieker, Christel; Schröder-Turk, Gerd E.; Mecke, Klaus; Spiecker, Erdmann

2015-01-01

The wing scales of the Green Hairstreak butterfly Callophrys rubi consist of crystalline domains with sizes of a few micrometers, which exhibit a congenitally handed porous chitin microstructure identified as the chiral triply periodic single-gyroid structure. Here, the chirality and crystallographic texture of these domains are investigated by means of electron tomography. The tomograms unambiguously reveal the coexistence of the two enantiomeric forms of opposite handedness: the left- and right-handed gyroids. These two enantiomers appear with nonequal probabilities, implying that molecularly chiral constituents of the biological formation process presumably invoke a chiral symmetry break, resulting in a preferred enantiomeric form of the gyroid structure. Assuming validity of the formation model proposed by Ghiradella H (1989) J Morphol 202(1):69–88 and Saranathan V, et al. (2010) Proc Natl Acad Sci USA 107(26):11676–11681, where the two enantiomeric labyrinthine domains of the gyroid are connected to the extracellular and intra-SER spaces, our findings imply that the structural chirality of the single gyroid is, however, not caused by the molecular chirality of chitin. Furthermore, the wing scales are found to be highly textured, with a substantial fraction of domains exhibiting the <001> directions of the gyroid crystal aligned parallel to the scale surface normal. Both findings are needed to completely understand the photonic purpose of the single gyroid in gyroid-forming butterflies. More importantly, they show the level of control that morphogenesis exerts over secondary features of biological nanostructures, such as chirality or crystallographic texture, providing inspiration for biomimetic replication strategies for synthetic self-assembly mechanisms. PMID:26438839
Coexistence of both gyroid chiralities in individual butterfly wing scales of Callophrys rubi.

PubMed

Winter, Benjamin; Butz, Benjamin; Dieker, Christel; Schröder-Turk, Gerd E; Mecke, Klaus; Spiecker, Erdmann

2015-10-20

The wing scales of the Green Hairstreak butterfly Callophrys rubi consist of crystalline domains with sizes of a few micrometers, which exhibit a congenitally handed porous chitin microstructure identified as the chiral triply periodic single-gyroid structure. Here, the chirality and crystallographic texture of these domains are investigated by means of electron tomography. The tomograms unambiguously reveal the coexistence of the two enantiomeric forms of opposite handedness: the left- and right-handed gyroids. These two enantiomers appear with nonequal probabilities, implying that molecularly chiral constituents of the biological formation process presumably invoke a chiral symmetry break, resulting in a preferred enantiomeric form of the gyroid structure. Assuming validity of the formation model proposed by Ghiradella H (1989) J Morphol 202(1):69-88 and Saranathan V, et al. (2010) Proc Natl Acad Sci USA 107(26):11676-11681, where the two enantiomeric labyrinthine domains of the gyroid are connected to the extracellular and intra-SER spaces, our findings imply that the structural chirality of the single gyroid is, however, not caused by the molecular chirality of chitin. Furthermore, the wing scales are found to be highly textured, with a substantial fraction of domains exhibiting the <001> directions of the gyroid crystal aligned parallel to the scale surface normal. Both findings are needed to completely understand the photonic purpose of the single gyroid in gyroid-forming butterflies. More importantly, they show the level of control that morphogenesis exerts over secondary features of biological nanostructures, such as chirality or crystallographic texture, providing inspiration for biomimetic replication strategies for synthetic self-assembly mechanisms.
Molecular motions that shape the cardiac action potential: Insights from voltage clamp fluorometry.

PubMed

Zhu, Wandi; Varga, Zoltan; Silva, Jonathan R

2016-01-01

Very recently, voltage-clamp fluorometry (VCF) protocols have been developed to observe the membrane proteins responsible for carrying the ventricular ionic currents that form the action potential (AP), including those carried by the cardiac Na(+) channel, NaV1.5, the L-type Ca(2+) channel, CaV1.2, the Na(+)/K(+) ATPase, and the rapid and slow components of the delayed rectifier, KV11.1 and KV7.1. This development is significant, because VCF enables simultaneous observation of ionic current kinetics with conformational changes occurring within specific channel domains. The ability gained from VCF, to connect nanoscale molecular movement to ion channel function has revealed how the voltage-sensing domains (VSDs) control ion flux through channel pores, mechanisms of post-translational regulation and the molecular pathology of inherited mutations. In the future, we expect that this data will be of great use for the creation of multi-scale computational AP models that explicitly represent ion channel conformations, connecting molecular, cell and tissue electrophysiology. Here, we review the VCF protocol, recent results, and discuss potential future developments, including potential use of these experimental findings to create novel computational models. Copyright © 2015 Elsevier Ltd. All rights reserved.
Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management.

PubMed

Grossmann, Sebastian; Nowak, Piotr; Neogi, Ujjwal

2015-01-01

HIV-1 near full-length genome (HIV-NFLG) sequencing from plasma is an attractive multidimensional tool to apply in large-scale population-based molecular epidemiological studies. It also enables genotypic resistance testing (GRT) for all drug target sites allowing effective intervention strategies for control and prevention in high-risk population groups. Thus, the main objective of this study was to develop a simplified subtype-independent, cost- and labour-efficient HIV-NFLG protocol that can be used in clinical management as well as in molecular epidemiological studies. Plasma samples (n=30) were obtained from HIV-1B (n=10), HIV-1C (n=10), CRF01_AE (n=5) and CRF01_AG (n=5) infected individuals with minimum viral load >1120 copies/ml. The amplification was performed with two large amplicons of 5.5 kb and 3.7 kb, sequenced with 17 primers to obtain HIV-NFLG. GRT was validated against ViroSeq™ HIV-1 Genotyping System. After excluding four plasma samples with low-quality RNA, a total of 26 samples were attempted. Among them, NFLG was obtained from 24 (92%) samples with the lowest viral load being 3000 copies/ml. High (>99%) concordance was observed between HIV-NFLG and ViroSeq™ when determining the drug resistance mutations (DRMs). The N384I connection mutation was additionally detected by NFLG in two samples. Our high efficiency subtype-independent HIV-NFLG is a simple and promising approach to be used in large-scale molecular epidemiological studies. It will facilitate the understanding of the HIV-1 pandemic population dynamics and outline effective intervention strategies. Furthermore, it can potentially be applicable in clinical management of drug resistance by evaluating DRMs against all available antiretrovirals in a single assay.
Probing multi-scale mechanical damage in connective tissues using X-ray diffraction.

PubMed

Bianchi, Fabio; Hofmann, Felix; Smith, Andrew J; Thompson, Mark S

2016-11-01

The accumulation of microstructural collagen damage following repetitive loading is linked to painful and debilitating tendon injuries. As a hierarchical, semi-crystalline material, collagen mechanics can be studied using X-ray diffraction. The aim of the study was to describe multi-structural changes in tendon collagen following controlled plastic damage (5% permanent strain). We used small angle X-ray scattering (SAXS) to interrogate the spacing of collagen molecules within a fibril, and wide angle X-ray scattering (WAXS) to measure molecular strains under macroscopic loading. Simultaneous recordings of SAXS and WAXS patterns, together with whole-tissue strain in physiologically hydrated rat-tail tendons were made during increments of in situ tensile loading. Results showed that while tissue level modulus was unchanged, fibril modulus decreased significantly, and molecular modulus significantly increased. Further, analysis of higher order SAXS peaks suggested structural changes in the gap and overlap regions, possibly localising the damage to molecular cross-links. Our results provide new insight into the fundamental damage processes at work in collagenous tissues and point to new directions for their mitigation and repair. This article reports the first in situ loading synchrotron studies on mechanical damage in collagenous tissues. We provide new insight into the nano- and micro-structural mechanisms of damage processes. Pre-damaged tendons showed differential alteration of moduli at macro, micro and nano-scales as measured using X-ray scattering techniques. Detailed analysis of higher order diffraction peaks suggested damage is localised to molecular cross-links. The results are consistent with previous X-ray scattering studies of tendons and also with recent thermal stability studies on damaged material. Detailed understanding of damage mechanisms is essential in the development of new therapies promoting tissue repair. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
Reliable determination of oxygen and hydrogen isotope ratios in atmospheric water vapour adsorbed on 3A molecular sieve.

PubMed

Han, Liang-Feng; Gröning, Manfred; Aggarwal, Pradeep; Helliker, Brent R

2006-01-01

The isotope ratio of atmospheric water vapour is determined by wide-ranging feedback effects from the isotope ratio of water in biological water pools, soil surface horizons, open water bodies and precipitation. Accurate determination of atmospheric water vapour isotope ratios is important for a broad range of research areas from leaf-scale to global-scale isotope studies. In spite of the importance of stable isotopic measurements of atmospheric water vapour, there is a paucity of published data available, largely because of the requirement for liquid nitrogen or dry ice for quantitative trapping of water vapour. We report results from a non-cryogenic method for quantitatively trapping atmospheric water vapour using 3A molecular sieve, although water is removed from the column using standard cryogenic methods. The molecular sieve column was conditioned with water of a known isotope ratio to 'set' the background signature of the molecular sieve. Two separate prototypes were developed, one for large collection volumes (3 mL) and one for small collection volumes (90 microL). Atmospheric water vapour was adsorbed to the column by pulling air through the column for several days to reach the desired final volume. Water was recovered from the column by baking at 250 degrees C in a dry helium or nitrogen air stream and cryogenically trapped. For the large-volume apparatus, the recovered water differed from water that was simultaneously trapped by liquid nitrogen (the experimental control) by 2.6 per thousand with a standard deviation (SD) of 1.5 per thousand for delta(2)H and by 0.3 per thousand with a SD of 0.2 per thousand for delta(18)O. Water-vapour recovery was not satisfactory for the small volume apparatus. Copyright (c) 2006 John Wiley & Sons, Ltd.
Study of Polymer Crystallization by Physical Vapor Deposition

NASA Astrophysics Data System (ADS)

Jeong, Hyuncheol

When a polymer is confined under the submicron length scale, confinement size and interfaces can significantly impact the crystallization kinetics and resulting morphology. The ability to tune the morphology of confined polymer systems is of critical importance for the development of high-performance polymer microelectronics. The wisdom from the research on confined crystallization suggests that it would be beneficial to have a processing route in which the crystallization of polymers is driven by interface and temperature effects at a nanometer-scale confinement. In practice, for atomic and small-molecular systems, physical vapor deposition (PVD) has been recognized as the most successful processing route for the precise control of the film structure at surface utilizing confinement effects. While standard PVD technologies are not generally applicable to the deposition of the chemically fragile macromolecules, the development of matrix-assisted pulsed laser evaporation (MAPLE) now enables the non-destructive PVD of high-molecular weight polymers. In this thesis work, we investigated the use of MAPLE for the precise control of the crystallization of polymer films at a molecular level. We also sought to decipher the rules governing the crystallization of confined polymers, by using MAPLE as a tool to form confined polymer systems onto substrates with a controlled temperature. We first explored the early stages of film growth and crystallization of poly(ethylene oxide) (PEO) at the substrate surface formed by MAPLE. The unique mechanism of film formation in MAPLE, the deposition of submicron-sized polymer droplets, allowed for the manifestation of confinement and substrate effects in the crystallization of MAPLE-deposited PEO. Furthermore, we also focused on the property of the amorphous PEO film formed by MAPLE, showing the dependence of polymer crystallization kinetics on the thermal history of the amorphous phase. Lastly, we probed how MAPLE processing affected the semi-crystalline structure in MAPLE-deposited polyethylene (PE) films. Depositing PE at various temperatures remarkably allowed for the tunability of the melting temperature and crystallinity of the PE films, thus manipulating the semi-crystalline structure. By comparing the structure of PE formed by different processing routes, i.e., MAPLE and melt-crystallization, we discussed how processing routes affect the development of semi-crystalline phase in polymer films.
TRACING THE MAGNETIC FIELD MORPHOLOGY OF THE LUPUS I MOLECULAR CLOUD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Franco, G. A. P.; Alves, F. O., E-mail: franco@fisica.ufmg.br, E-mail: falves@mpe.mpg.de

2015-07-01

Deep R-band CCD linear polarimetry collected for fields with lines of sight toward the Lupus I molecular cloud is used to investigate the properties of the magnetic field within this molecular cloud. The observed sample contains about 7000 stars, almost 2000 of them with a polarization signal-to-noise ratio larger than 5. These data cover almost the entire main molecular cloud and also sample two diffuse infrared patches in the neighborhood of Lupus I. The large-scale pattern of the plane-of-sky projection of the magnetic field is perpendicular to the main axis of Lupus I, but parallel to the two diffuse infraredmore » patches. A detailed analysis of our polarization data combined with the Herschel/SPIRE 350 μm dust emission map shows that the principal filament of Lupus I is constituted by three main clumps that are acted on by magnetic fields that have different large-scale structural properties. These differences may be the reason for the observed distribution of pre- and protostellar objects along the molecular cloud and the cloud’s apparent evolutionary stage. On the other hand, assuming that the magnetic field is composed of large-scale and turbulent components, we find that the latter is rather similar in all three clumps. The estimated plane-of-sky component of the large-scale magnetic field ranges from about 70 to 200 μG in these clumps. The intensity increases toward the Galactic plane. The mass-to-magnetic flux ratio is much smaller than unity, implying that Lupus I is magnetically supported on large scales.« less
The structure and statistics of interstellar turbulence

NASA Astrophysics Data System (ADS)

Kritsuk, A. G.; Ustyugov, S. D.; Norman, M. L.

2017-06-01

We explore the structure and statistics of multiphase, magnetized ISM turbulence in the local Milky Way by means of driven periodic box numerical MHD simulations. Using the higher order-accurate piecewise-parabolic method on a local stencil (PPML), we carry out a small parameter survey varying the mean magnetic field strength and density while fixing the rms velocity to observed values. We quantify numerous characteristics of the transient and steady-state turbulence, including its thermodynamics and phase structure, kinetic and magnetic energy power spectra, structure functions, and distribution functions of density, column density, pressure, and magnetic field strength. The simulations reproduce many observables of the local ISM, including molecular clouds, such as the ratio of turbulent to mean magnetic field at 100 pc scale, the mass and volume fractions of thermally stable Hi, the lognormal distribution of column densities, the mass-weighted distribution of thermal pressure, and the linewidth-size relationship for molecular clouds. Our models predict the shape of magnetic field probability density functions (PDFs), which are strongly non-Gaussian, and the relative alignment of magnetic field and density structures. Finally, our models show how the observed low rates of star formation per free-fall time are controlled by the multiphase thermodynamics and large-scale turbulence.
From boiling point to glass transition temperature: transport coefficients in molecular liquids follow three-parameter scaling.

PubMed

Schmidtke, B; Petzold, N; Kahlau, R; Hofmann, M; Rössler, E A

2012-10-01

The phenomenon of the glass transition is an unresolved problem in condensed matter physics. Its prominent feature, the super-Arrhenius temperature dependence of the transport coefficients, remains a challenge to be described over the full temperature range. For a series of molecular glass formers, we combined τ(T) collected from dielectric spectroscopy and dynamic light scattering covering a range 10(-12) s < τ(T) < 10(2) s. Describing the dynamics in terms of an activation energy E(T), we distinguish a high-temperature regime characterized by an Arrhenius law with a constant activation energy E(∞) and a low-temperature regime for which E(coop)(T) ≡ E(T)-E(∞) increases exponentially while cooling. A scaling is introduced, specifically E(coop)(T)/E(∞) [proportionality] exp[-λ(T/T(A)-1)], where λ is a fragility parameter and T(A) a reference temperature proportional to E(∞). In order to describe τ(T) still the attempt time τ(∞) has to be specified. Thus, a single interaction parameter E(∞) describing the high-temperature regime together with λ controls the temperature dependence of low-temperature cooperative dynamics.
Macroscopically Oriented Porous Materials with Periodic Ordered Structures: From Zeolites and Metal-Organic Frameworks to Liquid-Crystal-Templated Mesoporous Materials.

PubMed

Cho, Joonil; Ishida, Yasuhiro

2017-07-01

Porous materials with molecular-sized periodic structures, as exemplified by zeolites, metal-organic frameworks, or mesoporous silica, have attracted increasing attention due to their range of applications in storage, sensing, separation, and transformation of small molecules. Although the components of such porous materials have a tendency to pack in unidirectionally oriented periodic structures, such ideal types of packing cannot continue indefinitely, generally ceasing when they reach a micrometer scale. Consequently, most porous materials are composed of multiple randomly oriented domains, and overall behave as isotropic materials from a macroscopic viewpoint. However, if their channels could be unidirectionally oriented over a macroscopic scale, the resultant porous materials might serve as powerful tools for manipulating molecules. Guest molecules captured in macroscopically oriented channels would have their positions and directions well-defined, so that molecular events in the channels would proceed in a highly controlled manner. To realize such an ideal situation, numerous efforts have been made to develop various porous materials with macroscopically oriented channels. An overview of recent studies on the synthesis, properties, and applications of macroscopically oriented porous materials is presented. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Efficient parallel linear scaling construction of the density matrix for Born-Oppenheimer molecular dynamics.

PubMed

Mniszewski, S M; Cawkwell, M J; Wall, M E; Mohd-Yusof, J; Bock, N; Germann, T C; Niklasson, A M N

2015-10-13

We present an algorithm for the calculation of the density matrix that for insulators scales linearly with system size and parallelizes efficiently on multicore, shared memory platforms with small and controllable numerical errors. The algorithm is based on an implementation of the second-order spectral projection (SP2) algorithm [ Niklasson, A. M. N. Phys. Rev. B 2002 , 66 , 155115 ] in sparse matrix algebra with the ELLPACK-R data format. We illustrate the performance of the algorithm within self-consistent tight binding theory by total energy calculations of gas phase poly(ethylene) molecules and periodic liquid water systems containing up to 15,000 atoms on up to 16 CPU cores. We consider algorithm-specific performance aspects, such as local vs nonlocal memory access and the degree of matrix sparsity. Comparisons to sparse matrix algebra implementations using off-the-shelf libraries on multicore CPUs, graphics processing units (GPUs), and the Intel many integrated core (MIC) architecture are also presented. The accuracy and stability of the algorithm are illustrated with long duration Born-Oppenheimer molecular dynamics simulations of 1000 water molecules and a 303 atom Trp cage protein solvated by 2682 water molecules.

The Effect of Inappropriate Calibration: Three Case Studies in Molecular Ecology

PubMed Central

Ho, Simon Y. W.; Saarma, Urmas; Barnett, Ross; Haile, James; Shapiro, Beth

2008-01-01

Time-scales estimated from sequence data play an important role in molecular ecology. They can be used to draw correlations between evolutionary and palaeoclimatic events, to measure the tempo of speciation, and to study the demographic history of an endangered species. In all of these studies, it is paramount to have accurate estimates of time-scales and substitution rates. Molecular ecological studies typically focus on intraspecific data that have evolved on genealogical scales, but often these studies inappropriately employ deep fossil calibrations or canonical substitution rates (e.g., 1% per million years for birds and mammals) for calibrating estimates of divergence times. These approaches can yield misleading estimates of molecular time-scales, with significant impacts on subsequent evolutionary and ecological inferences. We illustrate this calibration problem using three case studies: avian speciation in the late Pleistocene, the demographic history of bowhead whales, and the Pleistocene biogeography of brown bears. For each data set, we compare the date estimates that are obtained using internal and external calibration points. In all three cases, the conclusions are significantly altered by the application of revised, internally-calibrated substitution rates. Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events. PMID:18286172
The effect of inappropriate calibration: three case studies in molecular ecology.

PubMed

Ho, Simon Y W; Saarma, Urmas; Barnett, Ross; Haile, James; Shapiro, Beth

2008-02-20

Time-scales estimated from sequence data play an important role in molecular ecology. They can be used to draw correlations between evolutionary and palaeoclimatic events, to measure the tempo of speciation, and to study the demographic history of an endangered species. In all of these studies, it is paramount to have accurate estimates of time-scales and substitution rates. Molecular ecological studies typically focus on intraspecific data that have evolved on genealogical scales, but often these studies inappropriately employ deep fossil calibrations or canonical substitution rates (e.g., 1% per million years for birds and mammals) for calibrating estimates of divergence times. These approaches can yield misleading estimates of molecular time-scales, with significant impacts on subsequent evolutionary and ecological inferences. We illustrate this calibration problem using three case studies: avian speciation in the late Pleistocene, the demographic history of bowhead whales, and the Pleistocene biogeography of brown bears. For each data set, we compare the date estimates that are obtained using internal and external calibration points. In all three cases, the conclusions are significantly altered by the application of revised, internally-calibrated substitution rates. Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events.
Physical properties and scaling relations of molecular clouds: the effect of stellar feedback

NASA Astrophysics Data System (ADS)

Grisdale, Kearn; Agertz, Oscar; Renaud, Florent; Romeo, Alessandro B.

2018-06-01

Using hydrodynamical simulations of entire galactic discs similar to the Milky Way, reaching 4.6{ pc} resolution, we study the origins of observed physical properties of giant molecular clouds (GMCs). We find that efficient stellar feedback is a necessary ingredient in order to develop a realistic interstellar medium (ISM), leading to molecular cloud masses, sizes, velocity dispersions and virial parameters in excellent agreement with Milky Way observations. GMC scaling relations observed in the Milky Way, such as the mass-size (M-R), velocity dispersion-size (σ-R), and the σ-RΣ relations, are reproduced in a feedback driven ISM when observed in projection, with M∝R2.3 and σ∝R0.56. When analysed in 3D, GMC scaling relations steepen significantly, indicating potential limitations of our understanding of molecular cloud 3D structure from observations. Furthermore, we demonstrate how a GMC population's underlying distribution of virial parameters can strongly influence the scatter in derived scaling relations. Finally, we show that GMCs with nearly identical global properties exist in different evolutionary stages, where a majority of clouds being either gravitationally bound or expanding, but with a significant fraction being compressed by external ISM pressure, at all times.
Theory of wavelet-based coarse-graining hierarchies for molecular dynamics.

PubMed

Rinderspacher, Berend Christopher; Bardhan, Jaydeep P; Ismail, Ahmed E

2017-07-01

We present a multiresolution approach to compressing the degrees of freedom and potentials associated with molecular dynamics, such as the bond potentials. The approach suggests a systematic way to accelerate large-scale molecular simulations with more than two levels of coarse graining, particularly applications of polymeric materials. In particular, we derive explicit models for (arbitrarily large) linear (homo)polymers and iterative methods to compute large-scale wavelet decompositions from fragment solutions. This approach does not require explicit preparation of atomistic-to-coarse-grained mappings, but instead uses the theory of diffusion wavelets for graph Laplacians to develop system-specific mappings. Our methodology leads to a hierarchy of system-specific coarse-grained degrees of freedom that provides a conceptually clear and mathematically rigorous framework for modeling chemical systems at relevant model scales. The approach is capable of automatically generating as many coarse-grained model scales as necessary, that is, to go beyond the two scales in conventional coarse-grained strategies; furthermore, the wavelet-based coarse-grained models explicitly link time and length scales. Furthermore, a straightforward method for the reintroduction of omitted degrees of freedom is presented, which plays a major role in maintaining model fidelity in long-time simulations and in capturing emergent behaviors.
Early Stage of Oxidation on Titanium Surface by Reactive Molecular Dynamics Simulation

DOE PAGES

Yang, Liang; Wang, C. Z.; Lin, Shiwei; ...

2018-01-01

Understanding of metal oxidation is very critical to corrosion control, catalysis synthesis, and advanced materials engineering. Metal oxidation is a very complex phenomenon, with many different processes which are coupled and involved from the onset of reaction. In this work, the initial stage of oxidation on titanium surface was investigated in atomic scale by molecular dynamics (MD) simulations using a reactive force field (ReaxFF). We show that oxygen transport is the dominant process during the initial oxidation. Our simulation also demonstrate that a compressive stress was generated in the oxide layer which blocked the oxygen transport perpendicular to the Titaniummore » (0001) surface and further prevented oxidation in the deeper layers. As a result, the mechanism of initial oxidation observed in this work can be also applicable to other self-limiting oxidation.« less
Bright Photon Upconversion on Composite Organic Lanthanide Molecules through Localized Thermal Radiation.

PubMed

Ye, Huanqing; Bogdanov, Viktor; Liu, Sheng; Vajandar, Saumitra; Osipowicz, Thomas; Hernández, Ignacio; Xiong, Qihua

2017-12-07

Converting low-energy photons via thermal radiation can be a potential approach for utilizing infrared (IR) photons to improve photovoltaic efficiency. Lanthanide-containing materials have achieved great progress in IR-to-visible photon upconversion (UC). Herein, we first report bright photon, tunable wavelength UC through localized thermal radiation at the molecular scale with low excitation power density (<10 W/cm 2 ) realized on lanthanide complexes of perfluorinated organic ligands. This is enabled by engineering the pathways of nonradiative de-excitation and energy transfer in a composite of ytterbium and terbium perfluoroimidodiphosphinates. The IR-excited thermal UC and wavelength control is realized through the terbium activators sensitized by the ytterbium sensitizers having high luminescence efficiency. The metallic molecular composite thus can be a potential energy material in the use of the IR solar spectrum for thermal photovoltaic applications.
Why many polymers are so fragile: A new perspective

DOE PAGES

Dalle-Ferrier, C.; Kisliuk, A.; Hong, L.; ...

2016-10-21

Many polymers exhibit much steeper temperature dependence of their structural relaxation time (higher fragility) than liquids of small molecules, and the mechanism of this unusually high fragility in polymers remains a puzzle. To reveal additional hints for understanding the underlying mechanism, we analyzed correlation of many properties of polymers to their fragility on example of model polymer polystyrene with various molecular weights (MWs). Here, we demonstrate that these correlations work for short chains (oligomers), but fail progressively with increase in MW. Our surprising discovery is that the steepness of the temperature dependence (fragility) of the viscosity that is determined bymore » chain relaxation follows the correlations at all molecular weights. These results suggest that the molecular level relaxation still follows the behavior usual for small molecules even in polymers, and its fragility (chain fragility) falls in the range usual for molecular liquids. It is the segmental relaxation that has this unusually high fragility. We also speculate that many polymers cannot reach an ergodic state on the time scale of segmental dynamics due to chain connectivity and rigidity. This leads to sharper decrease in accessible configurational entropy upon cooling and results in steeper temperature dependence of segmental relaxation. Our proposed scenario provides a new important insight into the specifics of polymer dynamics: the role of ergodicity time and length scale. At the end, we suggest that a similar scenario can be applicable also to other molecular systems with slow intra-molecular degrees of freedom and to chemically complex systems where the time scale of chemical fluctuations can be longer than the time scale of structural relaxation.« less
Why many polymers are so fragile: A new perspective

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dalle-Ferrier, C.; Kisliuk, A.; Hong, L.

Many polymers exhibit much steeper temperature dependence of their structural relaxation time (higher fragility) than liquids of small molecules, and the mechanism of this unusually high fragility in polymers remains a puzzle. To reveal additional hints for understanding the underlying mechanism, we analyzed correlation of many properties of polymers to their fragility on example of model polymer polystyrene with various molecular weights (MWs). Here, we demonstrate that these correlations work for short chains (oligomers), but fail progressively with increase in MW. Our surprising discovery is that the steepness of the temperature dependence (fragility) of the viscosity that is determined bymore » chain relaxation follows the correlations at all molecular weights. These results suggest that the molecular level relaxation still follows the behavior usual for small molecules even in polymers, and its fragility (chain fragility) falls in the range usual for molecular liquids. It is the segmental relaxation that has this unusually high fragility. We also speculate that many polymers cannot reach an ergodic state on the time scale of segmental dynamics due to chain connectivity and rigidity. This leads to sharper decrease in accessible configurational entropy upon cooling and results in steeper temperature dependence of segmental relaxation. Our proposed scenario provides a new important insight into the specifics of polymer dynamics: the role of ergodicity time and length scale. At the end, we suggest that a similar scenario can be applicable also to other molecular systems with slow intra-molecular degrees of freedom and to chemically complex systems where the time scale of chemical fluctuations can be longer than the time scale of structural relaxation.« less
Nanotechnology, resources, and pollution control

NASA Astrophysics Data System (ADS)

Gillett, Stephen L.

1996-09-01

The separation of different kinds of atoms or molecules from each other is a fundamental technological problem. Current techniques of resource extraction, which use the ancient paradigm of the differential partitioning of elements into coexisting phases, are simple but extremely wasteful and require feedstocks (`ores') that are already anomalously enriched. This is impractical for pollution control and desalination, which require extraction of low concentrations; instead, atomistic separation, typically by differential motion through semipermeable membranes, is used. The present application of such membranes is seriously limited, however, mostly because of limitations in their fabrication by conventional bulk techniques. The capabilities of biological systems, such as vertebrate kidneys, are vastly better, largely because they are intrinsically structured at a molecular scale. Nanofabrication of semipermeable membranes promises capabilities on the order of those of biological systems, and this in turn could provide much financial incentive for the development of molecular assemblers, as well established markets exist already. Continued incentives would exist, moreover, as markets expanded with decreasing costs, leading to such further applications as remediation of polluted sites, cheap desalination, and resource extraction from very low-grade sources.
Molecular Dynamics Studies of Proton Transport in Hydrogenase and Hydrogenase Mimics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ginovska-Pangovska, Bojana; Raugei, Simone; Shaw, Wendy J.

2016-08-02

Protons are used throughout the biological world for a number of functions, from charge balance to energy carriers. Metalloenzymes use protons as energy carriers and control proton movement both temporally and spatially. Despite the interest and need for controlled proton movement in other systems, the scientific community has not been able to develop extensive general rules for developing synthetic proton pathways. In part this is due to the challenging nature of studying these large and complex molecules experimentally, although experiments have gleaned extensive critical insight. While computational methods are also challenging because of the large size of the molecules, theymore » have been critical in advancing our knowledge of proton movement through pathways, but even further, they have advanced our knowledge in how protonation and proton movement is correlated with large and small scale molecular motions and electron movement. These studies often complement experimental studies but provide insight and depth simply not possible in many cases in the absence of theory. In this chapter, we will discuss advances and methods used in understanding proton movement in hydrogenases.« less
Role of solvent environments in single molecule conductance used insulator-modified mechanically controlled break junctions

NASA Astrophysics Data System (ADS)

Muthusubramanian, Nandini; Maity, Chandan; Galan Garcia, Elena; Eelkema, Rienk; Grozema, Ferdinand; van der Zant, Herre; Kavli Institute of Nanoscience Collaboration; Department of Chemical Engineering Collaboration

We present a method for studying the effects of polar solvents on charge transport through organic/biological single molecules by developing solvent-compatible mechanically controlled break junctions of gold coated with a thin layer of aluminium oxide using plasma enhanced atomic layer deposition (ALD). The optimal oxide thickness was experimentally determined to be 15 nm deposited at ALD operating temperature of 300°C which yielded atomically sharp electrodes and reproducible single-barrier tunnelling behaviour across a wide conductance range between 1 G0 and 10-7 G0. The insulator protected MCBJ devices were found to be effective in various solvents such as deionized water, phosphate buffered saline, methanol, acetonitrile and dichlorobenzene. The yield of molecular junctions using such insulated electrodes was tested by developing a chemical protocol for synthesizing an amphipathic form of oligo-phenylene ethynylene (OPE3-PEO) with thioacetate anchoring groups. This work has further applications in studying effects of solvation, dipole orientation and other thermodynamic interactions on charge transport. Eu Marie Curie Initial Training Network (ITN). MOLECULAR-SCALE ELECTRONICS: ``MOLESCO'' Project Number 606728.
Nanoimaging to Prevent and Treat Alzheimer’s and Parkinson’s Diseases. Scientific/Technical report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yuri L. Lyubchenko, PhD, DSc

2012-12-20

This project will develop innovative approaches to characterization of the very early stages of protein aggregation that eventually can be translated to the development of early diagnostic tools and efficient treatments for Alzheimer’s, Parkinson’s and Huntington’s diseases. Funding will be used to acquire nanoimaging technology for nanoscale imaging, manipulation and analysis of biomedical materials to develop treatments that will repair disabled proteins and cure diseases that result from protein malfunction, specifically Alzheimer’s and Parkinson’s diseases. Expected outcomes include tests for early diagnosis and therapeutic treatments for these devastating neurological diseases. To elucidate the mechanisms of protein misfolding, we will establishmore » an extensive program of experimental studies using a broad arsenal of advanced nanoscale and traditional techniques that will be integrated with molecular-scale modeling of protein misfolding and the nucleation of aggregate structures. To identify intracellular machinery or/and multicomponent complexes critically involved in protein misfolding, we will characterize interactions between targeted proteins and specific intracellular components or metabolites that impact on protein conformational pathways leading to protein misfolding accompanied by formation of toxic aggregated morphologies. To design innovative nanotechnology tools for the control of intracellular protein misfolding and aggregation processes, we will develop a predictive molecular scale model for intracellular protein misfolding and the formation of toxic aggregates. Verified through experimental studies, the objective is to establish an enabling foundation for the engineering of novel molecular diagnostics and therapeutics for various cellular pathologies.« less
Convergence acceleration of molecular dynamics methods for shocked materials using velocity scaling

NASA Astrophysics Data System (ADS)

Taylor, DeCarlos E.

2017-03-01

In this work, a convergence acceleration method applicable to extended system molecular dynamics techniques for shock simulations of materials is presented. The method uses velocity scaling to reduce the instantaneous value of the Rankine-Hugoniot conservation of energy constraint used in extended system molecular dynamics methods to more rapidly drive the system towards a converged Hugoniot state. When used in conjunction with the constant stress Hugoniostat method, the velocity scaled trajectories show faster convergence to the final Hugoniot state with little difference observed in the converged Hugoniot energy, pressure, volume and temperature. A derivation of the scale factor is presented and the performance of the technique is demonstrated using the boron carbide armour ceramic as a test material. It is shown that simulation of boron carbide Hugoniot states, from 5 to 20 GPa, using both a classical Tersoff potential and an ab initio density functional, are more rapidly convergent when the velocity scaling algorithm is applied. The accelerated convergence afforded by the current algorithm enables more rapid determination of Hugoniot states thus reducing the computational demand of such studies when using expensive ab initio or classical potentials.
General Formalism of Mass Scaling Approach for Replica-Exchange Molecular Dynamics and its Application

NASA Astrophysics Data System (ADS)

Nagai, Tetsuro

2017-01-01

Replica-exchange molecular dynamics (REMD) has demonstrated its efficiency by combining trajectories of a wide range of temperatures. As an extension of the method, the author formalizes the mass-manipulating replica-exchange molecular dynamics (MMREMD) method that allows for arbitrary mass scaling with respect to temperature and individual particles. The formalism enables the versatile application of mass-scaling approaches to the REMD method. The key change introduced in the novel formalism is the generalized rules for the velocity and momentum scaling after accepted replica-exchange attempts. As an application of this general formalism, the refinement of the viscosity-REMD (V-REMD) method [P. H. Nguyen, J. Chem. Phys. 132, 144109 (2010)] is presented. Numerical results are provided using a pilot system, demonstrating easier and more optimized applicability of the new version of V-REMD as well as the importance of adherence to the generalized velocity scaling rules. With the new formalism, more sound and efficient simulations will be performed.
Linear-scaling method for calculating nuclear magnetic resonance chemical shifts using gauge-including atomic orbitals within Hartree-Fock and density-functional theory.

PubMed

Kussmann, Jörg; Ochsenfeld, Christian

2007-08-07

Details of a new density matrix-based formulation for calculating nuclear magnetic resonance chemical shifts at both Hartree-Fock and density functional theory levels are presented. For systems with a nonvanishing highest occupied molecular orbital-lowest unoccupied molecular orbital gap, the method allows us to reduce the asymptotic scaling order of the computational effort from cubic to linear, so that molecular systems with 1000 and more atoms can be tackled with today's computers. The key feature is a reformulation of the coupled-perturbed self-consistent field (CPSCF) theory in terms of the one-particle density matrix (D-CPSCF), which avoids entirely the use of canonical MOs. By means of a direct solution for the required perturbed density matrices and the adaptation of linear-scaling integral contraction schemes, the overall scaling of the computational effort is reduced to linear. A particular focus of our formulation is to ensure numerical stability when sparse-algebra routines are used to obtain an overall linear-scaling behavior.
Moving Contact Lines: Linking Molecular Dynamics and Continuum-Scale Modeling.

PubMed

Smith, Edward R; Theodorakis, Panagiotis E; Craster, Richard V; Matar, Omar K

2018-05-17

Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular dynamics (MD) simulation has the ability to provide unique insight into the microscopic details that determine the dynamic behavior of the contact line, which is not possible with either continuum-scale simulations or experiments. On the other hand, continuum-based models provide a link to the macroscopic description of the system. In this Feature Article, we explore the complex range of physical factors, including the presence of surfactants, which governs the contact line motion through MD simulations. We also discuss links between continuum- and molecular-scale modeling and highlight the opportunities for future developments in this area.
Biomimetic Nanoarchitectures for the Study of T Cell Activation with Single-Molecule Control

NASA Astrophysics Data System (ADS)

Cai, Haogang

Physical factors in the environment of a cell affect its function and behavior in a variety of ways. There is increasing evidence that, among these factors, the geometric arrangement of receptor ligands plays an important role in setting the conditions for critical cellular processes. The goal of this thesis is to develop new techniques for probing the role of extracellular ligand geometry, with a focus on T cell activation. In this work, top-down molecular-scale nanofabrication and bottom-up selective self-assembly were combined in order to present functional nanomaterials (primarily biomolecules) on a surface with precise spatial control and single-molecule resolution. Such biomolecule nanoarrays are becoming an increasingly important tool in surface-based in vitro assays for biosensing, molecular and cellular studies. The nanoarrays consist of metallic nanodots patterned on glass coverslips using electron beam and nanoimprint lithography, combined with self-aligned pattern transfer. The nanodots were then used as anchors for the immobilization of biological ligands, and backfilled with a protein-repellent passivation layer of polyethylene glycol. The passivation efficiency was improved to minimize nonspecific adsorption. In order to ensure true single-molecule control, we developed an on-chip protocol to measure the molecular occupancy of nanodot arrays based on fluorescence photobleaching, while accounting for quenching effects by plasmonic absorption. We found that the molecular occupancy can be interpreted as a packing problem, with the solution depending on the nanodot size and the concentration of self-assembly reagents, where the latter can be easily adjusted to control the molecular occupancy according to the dot size. The optimized nanoarrays were used as biomimetic architectures for the study of T cell activation with single-molecule control. T cell activation involves an elaborate arrangement of signaling, adhesion, and costimulatory molecules organized into a stereotypic geometric structure, known as the immunological synapse, between T cell and antigen-presenting cell. Novel bifunctionalization schemes were developed to better mimic the antigen-presenting surfaces. Nanoarrays were functionalized by single molecules of UCHT1 Fab', and served as individual T cell receptor binding sites. The adhesion molecule ICAM-1 was bound to either static PEG background, or a mobile supported lipid bilayer. The minimum geometric requirements (receptor clustering, spacing and stoichiometry) for T cell activation was probed by systematic variation of the nanoarray spacing and cluster size. Out-of-plane spatial control of the two key molecules by way of nanopillar arrays was used to adjust the membrane bending and steric effects, which were essential for the investigation of molecular segregation in T cell activation. The results provide insights into the complicated T cell activation mechanism, with translational implications toward adoptive immunotherapies for cancer and other diseases. This single-molecule platform serves as a novel and powerful tool for molecular and cellular biology, e.g., receptor-mediated signaling/adhesion, especially when multiple ligands or membrane deformation are involved.
Bacteremia after supragingival scaling and dental extraction: Culture and molecular analyses.

PubMed

Reis, L C; Rôças, I N; Siqueira, J F; de Uzeda, M; Lacerda, V S; Domingues, Rmcp; Miranda, K R; Saraiva, R M

2018-05-01

To study the incidence and magnitude of bacteremia after dental extraction and supragingival scaling. Blood samples were taken before and 5 and 30 min after dental extraction and supragingival scaling from individuals at high (n = 44) or negligible risk (n = 51) for infective endocarditis. The former received prophylactic antibiotic therapy. Samples were subjected to aerobic and anaerobic culture and quantitative real-time polymerase chain reaction to determine the incidence of bacteremia and total bacterial levels. Patients who did not receive prophylactic antibiotic therapy had a higher incidence of positive blood cultures (30% 5 min after extraction) than patients who received prophylactic antibiotic therapy (0% 5 min after extraction; p < .01). Molecular analysis did not reveal significant differences in the incidence or magnitude of bacteremia between the two patient groups either 5 or 30 min after each of the procedures evaluated. Extraction was associated with higher incidence of bacteremia than supragingival scaling by blood culture (p = .03) and molecular analysis (p = .05). Molecular methods revealed that dental extraction and supragingival scaling were associated with similar incidence of bacteremia in groups receiving or not prophylactic antibiotic therapy. However, blood culture revealed that antibiotic therapy reduced viable cultivable bacteria in the bloodstream in the extraction group. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
IMPACT: Imaging and Molecular Markers for Patients with Lung Cancer: Approaches with Molecular Targets, Complementary/Innovative Treatments, and Therapeutic Modalities

DTIC Science & Technology

2016-04-01

Hypomagnesemia, Grade 3 in 1 patient • Hypokalemia, Grade 3 in 2 patient • Pneumonia , Grade 3 in 7 patients • Dehydration, Grade 3 in 3 patients. Once...improvements on lab- scale radiosynthesis (Fig. 9) so that it is readily scaled up and adopted by the cGMP manufacturing. We are working on an automated...reproducibly building at the nanometer scale , including the need for streamlined and “bottom-up” approaches for assembling nanoparticle architectures, the
The Future of Bio-technology

NASA Technical Reports Server (NTRS)

Trent, Jonathan

2005-01-01

Hosts of technologies, most notably in electronics, have been on the path of miniaturization for decades and in 2005 they have crossed the threshold of the nano-scale. Crossing the nano-scale threshold is a milestone in miniaturization, setting impressive new standards for component-packing densities. It also brings technology to a scale at which quantum effects and fault tolerance play significant roles and approaches the feasible physical limit form many conventional "top-down" manufacturing methods. I will suggest that the most formidable manufacturing problems in nanotechnology will be overcome and major breakthroughs will occur in a host of technologies, when nanotechnology converges with bio-technology; i.e. I will argue that the future of bio-technology is in nanotechnology. In 2005, methods in molecular biology, microscopy, bioinformatics, biochemistry, and genetic engineering have focused considerable attention on the nano-scale. On this scale, biology is a kind of recursive chemistry in which molecular recognition, self-assembly, self-organization and self-referencing context-control lead to the emergence of the complexity of structures and processes that are fundamental to all life forms. While we are still far from understanding this complexity, we are on the threshold of being able to use at least some of these biological properties for .technology. I will discuss the use of biomolecules, such as DNA, RNA, and proteins as "tools" for the bio-technologist of the future. More specifically, I will present in some detail an example of how we are using a genetically engineered 60-kDa protein (HSP60) from an organism living in near boiling sulfuric acid to build nano-scale templates for arranging metallic nanoparticles. These "extremophile" HSP60s self-assemble into robust double-ring structures called "chaperonins," which further assemble into filaments and arrays with nanometer accuracy. I will discuss our efforts to use chaperonins to organize quantum dots, electronic and magnetic nano-particles for electronic and photonic applications.

A Multi-Scale Approach to Airway Hyperresponsiveness: From Molecule to Organ

PubMed Central

Lauzon, Anne-Marie; Bates, Jason H. T.; Donovan, Graham; Tawhai, Merryn; Sneyd, James; Sanderson, Michael J.

2012-01-01

Airway hyperresponsiveness (AHR), a characteristic of asthma that involves an excessive reduction in airway caliber, is a complex mechanism reflecting multiple processes that manifest over a large range of length and time scales. At one extreme, molecular interactions determine the force generated by airway smooth muscle (ASM). At the other, the spatially distributed constriction of the branching airways leads to breathing difficulties. Similarly, asthma therapies act at the molecular scale while clinical outcomes are determined by lung function. These extremes are linked by events operating over intermediate scales of length and time. Thus, AHR is an emergent phenomenon that limits our understanding of asthma and confounds the interpretation of studies that address physiological mechanisms over a limited range of scales. A solution is a modular computational model that integrates experimental and mathematical data from multiple scales. This includes, at the molecular scale, kinetics, and force production of actin-myosin contractile proteins during cross-bridge and latch-state cycling; at the cellular scale, Ca2+ signaling mechanisms that regulate ASM force production; at the tissue scale, forces acting between contracting ASM and opposing viscoelastic tissue that determine airway narrowing; at the organ scale, the topographic distribution of ASM contraction dynamics that determine mechanical impedance of the lung. At each scale, models are constructed with iterations between theory and experimentation to identify the parameters that link adjacent scales. This modular model establishes algorithms for modeling over a wide range of scales and provides a framework for the inclusion of other responses such as inflammation or therapeutic regimes. The goal is to develop this lung model so that it can make predictions about bronchoconstriction and identify the pathophysiologic mechanisms having the greatest impact on AHR and its therapy. PMID:22701430
Nanostructures Enabled by On-Wire Lithography (OWL)

PubMed Central

Braunschweig, Adam B.; Schmucker, Abrin L.; Wei, Wei David; Mirkin, Chad A.

2010-01-01

Nanostructures fabricated by a novel technique, termed On-Wire-Lithography (OWL), can be combined with organic and biological molecules to create systems with emergent and highly functional properties. OWL is a template-based, electrochemical process for forming gapped cylindrical structures on a solid support, with feature sizes (both gap and segment length) that can be controlled on the sub-100 nm length scale. Structures prepared by this method have provided valuable insight into the plasmonic properties of noble metal nanomaterials and have formed the basis for novel molecular electronic, encoding, and biological detection devices. PMID:20396668
Self-assembled three-dimensional chiral colloidal architecture

NASA Astrophysics Data System (ADS)

Ben Zion, Matan Yah; He, Xiaojin; Maass, Corinna C.; Sha, Ruojie; Seeman, Nadrian C.; Chaikin, Paul M.

2017-11-01

Although stereochemistry has been a central focus of the molecular sciences since Pasteur, its province has previously been restricted to the nanometric scale. We have programmed the self-assembly of micron-sized colloidal clusters with structural information stemming from a nanometric arrangement. This was done by combining DNA nanotechnology with colloidal science. Using the functional flexibility of DNA origami in conjunction with the structural rigidity of colloidal particles, we demonstrate the parallel self-assembly of three-dimensional microconstructs, evincing highly specific geometry that includes control over position, dihedral angles, and cluster chirality.
Molecular biology of bladder cancer.

PubMed

Martin-Doyle, William; Kwiatkowski, David J

2015-04-01

Classic as well as more recent large-scale genomic analyses have uncovered multiple genes and pathways important for bladder cancer development. Genes involved in cell-cycle control, chromatin regulation, and receptor tyrosine and PI3 kinase-mammalian target of rapamycin signaling pathways are commonly mutated in muscle-invasive bladder cancer. Expression-based analyses have identified distinct types of bladder cancer that are similar to subsets of breast cancer, and have prognostic and therapeutic significance. These observations are leading to novel therapeutic approaches in bladder cancer, providing optimism for therapeutic progress. Copyright © 2015 Elsevier Inc. All rights reserved.
Pump-shaped dump optimal control reveals the nuclear reaction pathway of isomerization of a photoexcited cyanine dye.

PubMed

Dietzek, Benjamin; Brüggemann, Ben; Pascher, Torbjörn; Yartsev, Arkady

2007-10-31

Using optimal control as a spectroscopic tool we decipher the details of the molecular dynamics of the essential multidimensional excited-state photoisomerization - a fundamental chemical reaction of key importance in biology. Two distinct nuclear motions are identified in addition to the overall bond-twisting motion: Initially, the reaction is dominated by motion perpendicular to the torsion coordinate. At later times, a second optically active vibration drives the system along the reaction path to the bottom of the excited-state potential. The time scales of the wavepacket motion on a different part of the excited-state potential are detailed by pump-shaped dump optimal control. This technique offers new means to control a chemical reaction far from the Franck-Condon point of absorption and to map details of excited-state reaction pathways revealing unique insights into the underlying reaction mechanism.
Dynamic control of magnetic nanowires by light-induced domain-wall kickoffs

NASA Astrophysics Data System (ADS)

Heintze, Eric; El Hallak, Fadi; Clauß, Conrad; Rettori, Angelo; Pini, Maria Gloria; Totti, Federico; Dressel, Martin; Bogani, Lapo

2013-03-01

Controlling the speed at which systems evolve is a challenge shared by all disciplines, and otherwise unrelated areas use common theoretical frameworks towards this goal. A particularly widespread model is Glauber dynamics, which describes the time evolution of the Ising model and can be applied to any binary system. Here we show, using molecular nanowires under irradiation, that Glauber dynamics can be controlled by a novel domain-wall kickoff mechanism. In contrast to known processes, the kickoff has unambiguous fingerprints, slowing down the spin-flip attempt rate by several orders of magnitude, and following a scaling law. The required irradiance is very low, a substantial improvement over present methods of magneto-optical switching. These results provide a new way to control and study stochastic dynamic processes. Being general for Glauber dynamics, they can be extended to different kinds of magnetic nanowires and to numerous fields, ranging from social evolution to neural networks and chemical reactivity.
Experiment-scale molecular simulation study of liquid crystal thin films

NASA Astrophysics Data System (ADS)

Nguyen, Trung Dac; Carrillo, Jan-Michael Y.; Matheson, Michael A.; Brown, W. Michael

2014-03-01

Supercomputers have now reached a performance level adequate for studying thin films with molecular detail at the relevant scales. By exploiting the power of GPU accelerators on Titan, we have been able to perform simulations of characteristic liquid crystal films that provide remarkable qualitative agreement with experimental images. We have demonstrated that key features of spinodal instability can only be observed with sufficiently large system sizes, which were not accessible with previous simulation studies. Our study emphasizes the capability and significance of petascale simulations in providing molecular-level insights in thin film systems as well as other interfacial phenomena.
Probing the Reproducibility of Leaf Growth and Molecular Phenotypes: A Comparison of Three Arabidopsis Accessions Cultivated in Ten Laboratories1[W

PubMed Central

Massonnet, Catherine; Vile, Denis; Fabre, Juliette; Hannah, Matthew A.; Caldana, Camila; Lisec, Jan; Beemster, Gerrit T.S.; Meyer, Rhonda C.; Messerli, Gaëlle; Gronlund, Jesper T.; Perkovic, Josip; Wigmore, Emma; May, Sean; Bevan, Michael W.; Meyer, Christian; Rubio-Díaz, Silvia; Weigel, Detlef; Micol, José Luis; Buchanan-Wollaston, Vicky; Fiorani, Fabio; Walsh, Sean; Rinn, Bernd; Gruissem, Wilhelm; Hilson, Pierre; Hennig, Lars; Willmitzer, Lothar; Granier, Christine

2010-01-01

A major goal of the life sciences is to understand how molecular processes control phenotypes. Because understanding biological systems relies on the work of multiple laboratories, biologists implicitly assume that organisms with the same genotype will display similar phenotypes when grown in comparable conditions. We investigated to what extent this holds true for leaf growth variables and metabolite and transcriptome profiles of three Arabidopsis (Arabidopsis thaliana) genotypes grown in 10 laboratories using a standardized and detailed protocol. A core group of four laboratories generated similar leaf growth phenotypes, demonstrating that standardization is possible. But some laboratories presented significant differences in some leaf growth variables, sometimes changing the genotype ranking. Metabolite profiles derived from the same leaf displayed a strong genotype × environment (laboratory) component. Genotypes could be separated on the basis of their metabolic signature, but only when the analysis was limited to samples derived from one laboratory. Transcriptome data revealed considerable plant-to-plant variation, but the standardization ensured that interlaboratory variation was not considerably larger than intralaboratory variation. The different impacts of the standardization on phenotypes and molecular profiles could result from differences of temporal scale between processes involved at these organizational levels. Our findings underscore the challenge of describing, monitoring, and precisely controlling environmental conditions but also demonstrate that dedicated efforts can result in reproducible data across multiple laboratories. Finally, our comparative analysis revealed that small variations in growing conditions (light quality principally) and handling of plants can account for significant differences in phenotypes and molecular profiles obtained in independent laboratories. PMID:20200072
Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations.

PubMed

Salvalaglio, Matteo; Tiwary, Pratyush; Maggioni, Giovanni Maria; Mazzotti, Marco; Parrinello, Michele

2016-12-07

Condensation of a liquid droplet from a supersaturated vapour phase is initiated by a prototypical nucleation event. As such it is challenging to compute its rate from atomistic molecular dynamics simulations. In fact at realistic supersaturation conditions condensation occurs on time scales that far exceed what can be reached with conventional molecular dynamics methods. Another known problem in this context is the distortion of the free energy profile associated to nucleation due to the small, finite size of typical simulation boxes. In this work the problem of time scale is addressed with a recently developed enhanced sampling method while contextually correcting for finite size effects. We demonstrate our approach by studying the condensation of argon, and showing that characteristic nucleation times of the order of magnitude of hours can be reliably calculated. Nucleation rates spanning a range of 10 orders of magnitude are computed at moderate supersaturation levels, thus bridging the gap between what standard molecular dynamics simulations can do and real physical systems.
Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations

NASA Astrophysics Data System (ADS)

Salvalaglio, Matteo; Tiwary, Pratyush; Maggioni, Giovanni Maria; Mazzotti, Marco; Parrinello, Michele

2016-12-01

Condensation of a liquid droplet from a supersaturated vapour phase is initiated by a prototypical nucleation event. As such it is challenging to compute its rate from atomistic molecular dynamics simulations. In fact at realistic supersaturation conditions condensation occurs on time scales that far exceed what can be reached with conventional molecular dynamics methods. Another known problem in this context is the distortion of the free energy profile associated to nucleation due to the small, finite size of typical simulation boxes. In this work the problem of time scale is addressed with a recently developed enhanced sampling method while contextually correcting for finite size effects. We demonstrate our approach by studying the condensation of argon, and showing that characteristic nucleation times of the order of magnitude of hours can be reliably calculated. Nucleation rates spanning a range of 10 orders of magnitude are computed at moderate supersaturation levels, thus bridging the gap between what standard molecular dynamics simulations can do and real physical systems.
Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schulz, Roland; Lindner, Benjamin; Petridis, Loukas

2009-01-01

A strategy is described for a fast all-atom molecular dynamics simulation of multimillion-atom biological systems on massively parallel supercomputers. The strategy is developed using benchmark systems of particular interest to bioenergy research, comprising models of cellulose and lignocellulosic biomass in an aqueous solution. The approach involves using the reaction field (RF) method for the computation of long-range electrostatic interactions, which permits efficient scaling on many thousands of cores. Although the range of applicability of the RF method for biomolecular systems remains to be demonstrated, for the benchmark systems the use of the RF produces molecular dipole moments, Kirkwood G factors,more » other structural properties, and mean-square fluctuations in excellent agreement with those obtained with the commonly used Particle Mesh Ewald method. With RF, three million- and five million atom biological systems scale well up to 30k cores, producing 30 ns/day. Atomistic simulations of very large systems for time scales approaching the microsecond would, therefore, appear now to be within reach.« less
Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer.

PubMed

Schulz, Roland; Lindner, Benjamin; Petridis, Loukas; Smith, Jeremy C

2009-10-13

A strategy is described for a fast all-atom molecular dynamics simulation of multimillion-atom biological systems on massively parallel supercomputers. The strategy is developed using benchmark systems of particular interest to bioenergy research, comprising models of cellulose and lignocellulosic biomass in an aqueous solution. The approach involves using the reaction field (RF) method for the computation of long-range electrostatic interactions, which permits efficient scaling on many thousands of cores. Although the range of applicability of the RF method for biomolecular systems remains to be demonstrated, for the benchmark systems the use of the RF produces molecular dipole moments, Kirkwood G factors, other structural properties, and mean-square fluctuations in excellent agreement with those obtained with the commonly used Particle Mesh Ewald method. With RF, three million- and five million-atom biological systems scale well up to ∼30k cores, producing ∼30 ns/day. Atomistic simulations of very large systems for time scales approaching the microsecond would, therefore, appear now to be within reach.
Quantitative Resistance: More Than Just Perception of a Pathogen.

PubMed

Corwin, Jason A; Kliebenstein, Daniel J

2017-04-01

Molecular plant pathology has focused on studying large-effect qualitative resistance loci that predominantly function in detecting pathogens and/or transmitting signals resulting from pathogen detection. By contrast, less is known about quantitative resistance loci, particularly the molecular mechanisms controlling variation in quantitative resistance. Recent studies have provided insight into these mechanisms, showing that genetic variation at hundreds of causal genes may underpin quantitative resistance. Loci controlling quantitative resistance contain some of the same causal genes that mediate qualitative resistance, but the predominant mechanisms of quantitative resistance extend beyond pathogen recognition. Indeed, most causal genes for quantitative resistance encode specific defense-related outputs such as strengthening of the cell wall or defense compound biosynthesis. Extending previous work on qualitative resistance to focus on the mechanisms of quantitative resistance, such as the link between perception of microbe-associated molecular patterns and growth, has shown that the mechanisms underlying these defense outputs are also highly polygenic. Studies that include genetic variation in the pathogen have begun to highlight a potential need to rethink how the field considers broad-spectrum resistance and how it is affected by genetic variation within pathogen species and between pathogen species. These studies are broadening our understanding of quantitative resistance and highlighting the potentially vast scale of the genetic basis of quantitative resistance. © 2017 American Society of Plant Biologists. All rights reserved.
Synthetic Motors and Nanomachines.

NASA Astrophysics Data System (ADS)

Flood, Amar

2006-03-01

A bistable and palindromically-constituted [3]rotaxane incorporating two mechanically-mobile rings interlocked around a linear dumbbell component, has been designed to operate like the sarcomeres of skeletal muscle. Contraction and extension occurs when the inter-ring distance of the two rings switch, ideally, between 4.2 and 1.4 nm upon redox stimulation either chemically or electrochemically in the solution phase. When the mobile rings of these artificial molecular muscles are bound onto the tops of gold-coated, micron-scale cantilever beams, their controllable nanometer motions have a chance to be amplified along the long axis of each cantilever. It turns out that ˜6 billion of the self-assembled [3]rotaxanes can bend the cantilevers in a bistable manner concomitant with the cycled addition of redox agents. The extent of bending is commensurate with 10's of pN of force per [3]rotaxane. Recent studies on a set of ``single-shot'' control [2]rotaxanes have provided additional evidence for the origins of the force generation as it arises from a molecule-based electrostatic repulsion energy of about 10 kcal/mol at 300 K. These findings will be presented in terms of the underlying thermodynamics and kinetics that have been utilized extensively to direct the design and synthesis of artificial molecular machines and which may also serve as a guide for the rational design of unidirectional molecular motors.
Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

NASA Astrophysics Data System (ADS)

Negre, Christian

2017-06-01

A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.
Polymeric molecular sieve membranes via in situ cross-linking of non-porous polymer membrane templates.

PubMed

Qiao, Zhen-An; Chai, Song-Hai; Nelson, Kimberly; Bi, Zhonghe; Chen, Jihua; Mahurin, Shannon M; Zhu, Xiang; Dai, Sheng

2014-04-16

High-performance polymeric membranes for gas separation are attractive for molecular-level separations in industrial-scale chemical, energy and environmental processes. Molecular sieving materials are widely regarded as the next-generation membranes to simultaneously achieve high permeability and selectivity. However, most polymeric molecular sieve membranes are based on a few solution-processable polymers such as polymers of intrinsic microporosity. Here we report an in situ cross-linking strategy for the preparation of polymeric molecular sieve membranes with hierarchical and tailorable porosity. These membranes demonstrate exceptional performance as molecular sieves with high gas permeabilities and selectivities for smaller gas molecules, such as carbon dioxide and oxygen, over larger molecules such as nitrogen. Hence, these membranes have potential for large-scale gas separations of commercial and environmental relevance. Moreover, this strategy could provide a possible alternative to 'classical' methods for the preparation of porous membranes and, in some cases, the only viable synthetic route towards certain membranes.
Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales

PubMed Central

Ayton, Gary S.; Lyman, Edward

2014-01-01

An overall multiscale simulation strategy for large scale coarse-grain simulations of membrane protein systems is presented. The protein is modeled as a heterogeneous elastic network, while the lipids are modeled using the hybrid analytic-systematic (HAS) methodology, where in both cases atomistic level information obtained from molecular dynamics simulation is used to parameterize the model. A feature of this approach is that from the outset liposome length scales are employed in the simulation (i.e., on the order of ½ a million lipids plus protein). A route to develop highly coarse-grained models from molecular-scale information is proposed and results for N-BAR domain protein remodeling of a liposome are presented. PMID:20158037
Precise measurement of the self-diffusion coefficient for poly(ethylene glycol) in aqueous solution using uniform oligomers

NASA Astrophysics Data System (ADS)

Shimada, Kayori; Kato, Haruhisa; Saito, Takeshi; Matsuyama, Shigetomo; Kinugasa, Shinichi

2005-06-01

Uniform poly(ethylene glycol) (PEG) oligomers, with a degree of polymerization n =1-40, were separated by preparative supercritical fluid chromatography from commercial monodispersed samples. Diffusion coefficients, D, for separated uniform PEG oligomers were measured in dilute solutions of deuterium oxide (D2O) at 30 ° C, using pulsed-field gradient nuclear magnetic resonance. The measured D for each molecular weight was extrapolated to infinite dilution. Diffusion coefficients obtained at infinite dilution follow the scaling behavior of Zimm-type diffusion, even in the lower molecular weight range. Molecular-dynamics simulations for PEG in H2O also showed this scaling behavior, and reproduced close hydrodynamic interactions between PEG and water. These findings suggest that diffusion of PEG in water is dominated by hydrodynamic interaction over a wide molecular weight range, including at low molecular weights around 1000.
Covalent Binding with Neutrons on the Femto-scale

NASA Astrophysics Data System (ADS)

von Oertzen, W.; Kanada-En'yo, Y.; Kimura, M.

2017-06-01

In light nuclei we have well defined clusters, nuclei with closed shells, which serve as centers for binary molecules with covalent binding by valence neutrons. Single neutron orbitals in light neutron-excess nuclei have well defined shell model quantum numbers. With the combination of two clusters and their neutron valence states, molecular two-center orbitals are defined; in the two-center shell model we can place valence neutrons in a large variety of molecular two-center states, and the formation of Dimers becomes possible. The corresponding rotational bands point with their large moments of inertia and the Coriolis decoupling effect (for K = 1/2 bands) to the internal molecular orbital structure in these states. On the basis of these the neutron rich isotopes allow the formation of a large variety molecular structures on the nuclear scale. An extended Ikeda diagram can be drawn for these cases. Molecular bands in Be and Ne-isotopes are discussed as text-book examples.
Update on N2O4 Molecular Sieving with 3A Material at NASA/KSC

NASA Technical Reports Server (NTRS)

Davis, Chuck; Dorn, Claudia

2000-01-01

During its operational life, the Shuttle Program has experienced numerous failures in the Nitrogen Tetroxide (N2O4) portion of Reaction Control System (RCS), many of which were attributed to iron-nitrate contamination. Since the mid-1980's, N2O4 has been processed through a molecular sieve at the N2O4 manufacturer's facility which results in an iron content typically less than 0.5 parts-per-million-by-weight (ppmw). In February 1995, a Tiger Team was formed to attempt to resolve the iron nitrate problem. Eighteen specific actions were recommended as possibly reducing system failures. Those recommended actions include additional N2O4 molecular sieving at the Shuttle launch site. Testing at NASA White Sands Test Facility (WSTF) determined an alternative molecular sieve material could also reduce the water-equivalent content (free water and HNO3) and thereby further reduce the natural production of iron nitrate in N2O4 while stored in iron-alloy storage tanks. Since April '96, NASA Kennedy Space Center (KSC) has been processing N2O4 through the alternative molecular sieve material prior to delivery to Shuttle launch pad N2O4 storage tanks. A new, much larger capacity molecular sieve unit has also been used. This paper will evaluate the effectiveness of N2O4 molecular sieving on a large-scale basis and attempt to determine if the resultant lower-iron and lower-water content N2O4 maintains this new purity level in pad storage tanks and shuttle flight systems.

Molecular-Scale Investigation of Heavy Metal Ions at a Charged Langmuir Monolayer

NASA Astrophysics Data System (ADS)

Rock, William; Qiao, Baofu; Uysal, Ahmet; Bu, Wei; Lin, Binhua

Solvent extraction - the surfactant-aided preferential transfer of a species from an aqueous to an organic phase - is an important technique used in heavy and precious metal refining and reprocessing. Solvent extraction requires transfer through an oil/water interface, and interfacial interactions are expected to control transfer kinetics and phase stability, yet these key interactions are poorly understood. Langmuir monolayers with charged headgroups atop concentrated salt solutions containing heavy metal ions act as a model of solvent extraction interfaces; studies of ions at a charged surface are also fundamentally important to many other phenomena including protein solvation, mineral surface chemistry, and electrochemistry. We probe these charged interfaces using a variety of surface-sensitive techniques - vibrational sum frequency generation (VSFG) spectroscopy, x-ray reflectivity (XRR), x-ray fluorescence near total reflection (XFNTR), and grazing incidence diffraction (GID). We integrate experiments with Molecular Dynamics (MD) simulations to uncover the molecular-level interfacial structure. This work is supported by the U.S. DOE, BES, Contract DE-AC02-06CH11357. ChemMatCARS is supported by NSF/CHE-1346572.
Stable Organic Monolayers on Oxide-Free Silicon/Germanium in a Supercritical Medium: A New Route to Molecular Electronics.

PubMed

Puniredd, Sreenivasa Reddy; Jayaraman, Sundaramurthy; Yeong, Sai Hooi; Troadec, Cedric; Srinivasan, M P

2013-05-02

Oxide-free Si and Ge surfaces have been passivated and modified with organic molecules by forming covalent bonds between the surfaces and reactive end groups of linear alkanes and aromatic species using single-step deposition in supercritical carbon dioxide (SCCO2). The process is suitable for large-scale manufacturing due to short processing times, simplicity, and high resistance to oxidation. It also allows the formation of monolayers with varying reactive terminal groups, thus enabling formation of nanostructures engineered at the molecular level. Ballistic electron emission microscopy (BEEM) spectra performed on the organic monolayer on oxide-free silicon capped by a thin gold layer reveals for the first time an increase in transmission of the ballistic current through the interface of up to three times compared to a control device, in contrast to similar studies reported in the literature suggestive of oxide-free passivation in SCCO2. The SCCO2 process combined with the preliminary BEEM results opens up new avenues for interface engineering, leading to molecular electronic devices.
Highly Polarized Fluorescent Illumination Using Liquid Crystal Phase.

PubMed

Gim, Min-Jun; Turlapati, Srikanth; Debnath, Somen; Rao, Nandiraju V S; Yoon, Dong Ki

2016-02-10

Liquid crystal (LC) materials are currently the dominant electronic materials in display technology because of the ease of control of molecular orientation using an electric field. However, this technology requires the fabrication of two polarizers to create operational displays, reducing light transmission efficiency below 10%. It is therefore desirable to develop new technologies to enhance the light efficiency while maintaining or improving other properties such as the modulation speed of the molecular orientation. Here we report a uniaxial-oriented B7 smectic liquid crystalline film, using fluorescent bent-core LC molecules, a chemically modified substrate, and an in-plane electric field. A LC droplet under homeotropic boundary conditions of air/LC as well as LC/substrate exhibits large focal conic like optical textures. The in-plane electric field induced uniaxial orientation of the LC molecules, in which molecular polar directors are aligned in the direction of the electric field. This highly oriented LC film exhibits linearly polarized luminescence and microsecond time-scale modulation characteristics. The resultant device is both cheap and easy to fabricate and thus has great potential for electro-optic applications, including LC displays, bioimaging systems, and optical communications.
Motion of Molecular Probes and Viscosity Scaling in Polyelectrolyte Solutions at Physiological Ionic Strength

PubMed Central

Sozanski, Krzysztof; Wisniewska, Agnieszka; Kalwarczyk, Tomasz; Sznajder, Anna; Holyst, Robert

2016-01-01

We investigate transport properties of model polyelectrolyte systems at physiological ionic strength (0.154 M). Covering a broad range of flow length scales—from diffusion of molecular probes to macroscopic viscous flow—we establish a single, continuous function describing the scale dependent viscosity of high-salt polyelectrolyte solutions. The data are consistent with the model developed previously for electrically neutral polymers in a good solvent. The presented approach merges the power-law scaling concepts of de Gennes with the idea of exponential length scale dependence of effective viscosity in complex liquids. The result is a simple and applicable description of transport properties of high-salt polyelectrolyte solutions at all length scales, valid for motion of single molecules as well as macroscopic flow of the complex liquid. PMID:27536866
Optical control of antibacterial activity

NASA Astrophysics Data System (ADS)

Velema, Willem A.; van der Berg, Jan Pieter; Hansen, Mickel J.; Szymanski, Wiktor; Driessen, Arnold J. M.; Feringa, Ben L.

2013-11-01

Bacterial resistance is a major problem in the modern world, stemming in part from the build-up of antibiotics in the environment. Novel molecular approaches that enable an externally triggered increase in antibiotic activity with high spatiotemporal resolution and auto-inactivation are highly desirable. Here we report a responsive, broad-spectrum, antibacterial agent that can be temporally activated with light, whereupon it auto-inactivates on the scale of hours. The use of such a ‘smart’ antibiotic might prevent the build-up of active antimicrobial material in the environment. Reversible optical control over active drug concentration enables us to obtain pharmacodynamic information. Precisely localized control of activity is achieved, allowing the growth of bacteria to be confined to defined patterns, which has potential for the development of treatments that avoid interference with the endogenous microbial population in other parts of the organism.
Energetic basis for the molecular-scale organization of bone

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tao, Jinhui; Battle, Keith C.; Pan, Haihua

2014-12-24

The remarkable properties of bone derive from a highly organized arrangement of co-aligned nm-scale apatite platelets within a fibrillar collagen matrix. The origin of this arrangement is poorly understood and the crystal structures of hydroxyapatite (HAP) and the non-mineralized collagen fibrils alone do not provide an explanation. Moreover, little is known about collagen-apatite interaction energies, which should strongly influence both the molecular-scale organization and the resulting mechanical properties of the composite. We investigated collagen-mineral interactions by combining dynamic force spectroscopy (DFS) measurements of binding energies with molecular dynamics (MD) simulations of binding and AFM observations of collagen adsorption on singlemore » crystals of calcium phosphate for four mineral phases of potential importance in bone formation. In all cases, we observe a strong preferential orientation of collagen binding, but comparison between the observed orientations and TEM analyses native tissues shows only calcium-deficient apatite (CDAP) provides an interface with collagen that is consistent with both. MD simulations predict preferred collagen orientations that agree with observations and results from both MD and DFS reveal large values for the binding energy due to multiple binding sites. These findings reconcile apparent contradictions inherent in a hydroxyapatite or carbonated apatite (CAP) model of bone mineral and provide an energetic rationale for the molecular scale organization of bone.« less
Energetic basis for the molecular-scale organization of bone

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tao, Jinhui; Battle, Keith C.; Pan, Haihua

The remarkable properties of bone derive from a highly organized arrangement of co-aligned nm-scale apatite platelets within a fibrillar collagen matrix. The origin of this arrangement is poorly understood and the crystal structures of hydroxyapatite (HAP) and the non-mineralized collagen fibrils alone do not provide an explanation. Moreover, little is known about collagen-apatite interaction energies, which should strongly influence both the molecular-scale organization and the resulting mechanical properties of the composite. We investigated collagen-mineral interactions by combining dynamic force spectroscopy (DFS) measurements of binding energies with molecular dynamics (MD) simulations of binding and AFM observations of collagen adsorption on singlemore » crystals of calcium phosphate for four mineral phases of potential importance in bone formation. In all cases, we observe a strong preferential orientation of collagen binding, but comparison between the observed orientations and TEM analyses native tissues shows only calcium-deficient apatite (CDAP) provides an interface with collagen that is consistent with both. MD simulations predict preferred collagen orientations that agree with observations and results from both MD and DFS reveal large values for the binding energy due to multiple binding sites. These findings reconcile apparent contradictions inherent in a hydroxyapatite or carbonated apatite (CAP) model of bone mineral and provide an energetic rationale for the molecular scale organization of bone.« less
Accelerating the Use of Molecular Modeling in the High School Classroom with VMD Lite

ERIC Educational Resources Information Center

Lundquist, Karl; Herndon, Conner; Harty, Tyson H.; Gumbart, James C.

2016-01-01

It is often difficult for students to develop an intuition about molecular processes, which occur in a realm far different from day-to-day life. For example, thermal fluctuations take on hurricane-like proportions at the molecular scale. Students need a way to visualize realistic depictions of molecular processes to appreciate them. To this end,…
Properties of PMR Polyimides Improved by Preparation of Polyhedral Oligomeric Silsesquioxane (POSS) Nanocomposites

NASA Technical Reports Server (NTRS)

Campbell, Sandi G.; Lee, Andre

2005-01-01

The field of hybrid organic-inorganic materials has grown drastically over the last several years. This interest stems from our ever-increasing ability to custom-build and control molecular structure at several length scales. This ability to control both the composition and structure of hybrid materials is sometimes broadly referred to as nanocomposite systems. One class of hybrid (organic-inorganic) nanostructured material is polyhedral oligomeric silsesquioxane (POSS), shown in the preceding diagram. The hybrid composition gives POSS materials dramatically enhanced properties relative to traditional hydrocarbons and inorganics. An important benefit of this technology is that it makes possible the formulations of nanostructured chemicals with excellent thermal and oxidative stability. This is largely due to the inorganic component.
Advances in modelling of biomimetic fluid flow at different scales

PubMed Central

2011-01-01

The biomimetic flow at different scales has been discussed at length. The need of looking into the biological surfaces and morphologies and both geometrical and physical similarities to imitate the technological products and processes has been emphasized. The complex fluid flow and heat transfer problems, the fluid-interface and the physics involved at multiscale and macro-, meso-, micro- and nano-scales have been discussed. The flow and heat transfer simulation is done by various CFD solvers including Navier-Stokes and energy equations, lattice Boltzmann method and molecular dynamics method. Combined continuum-molecular dynamics method is also reviewed. PMID:21711847
Intermolecular and interfacial forces: Elucidating molecular mechanisms using chemical force microscopy

NASA Astrophysics Data System (ADS)

Ashby, Paul David

Investigation into the origin of forces dates to the early Greeks. Yet, only in recent decades have techniques for elucidating the molecular origin of forces been developed. Specifically, Chemical Force Microscopy uses the high precision and nanometer scale probe of Atomic Force Microscopy to measure molecular and interfacial interactions. This thesis presents the development of many novel Chemical Force Microscopy techniques for measuring equilibrium and time-dependant force profiles of molecular interactions, which led to a greater understanding of the origin of interfacial forces in solution. In chapter 2, Magnetic Feedback Chemical Force Microscopy stiffens the cantilever for measuring force profiles between self-assembled monolayer (SAM) surfaces. Hydroxyl and carboxyl terminated SAMs produce long-range interactions that extend one or three nanometers into the solvent, respectively. In chapter 3, an ultra low noise AFM is produced through multiple modifications to the optical deflection detection system and signal processing electronics. In chapter 4, Brownian Force Profile Reconstruction is developed for accurate measurement of steep attractive interactions. Molecular ordering is observed for OMCTS, 1-nonanol, and water near flat surfaces. The molecular ordering of the solvent produces structural or solvation forces, providing insight into the orientation and possible solidification of the confined solvent. Seven molecular layers of OMCTS are observed but the oil remains fluid to the last layer. 1-nonanol strongly orders near the surface and becomes quasi-crystalline with four layers. Water is oriented by the surface and symmetry requires two layers of water (3.7 A) to be removed simultaneously. In chapter 5, electronic control of the cantilever Q (Q-control) is used to obtain the highest imaging sensitivity. In chapter 6, Energy Dissipation Chemical Force Microscopy is developed to investigate the time dependence and dissipative characteristics of SAM interfacial interactions in solution. Long-range adhesive forces for hydroxyl and carboxyl terminated SAM surfaces arise from solvent, not ionic, interactions. Exclusion of the solvent and contact between the SAM surfaces leads to rearrangement of the SAM headgroups. The isolation of the chemical and physical interfacial properties from the topography by Energy Dissipation Chemical Force Microscopy produces a new quantitative high-sensitivity imaging mode.
Spatially Different Tissue-Scale Diffusivity Shapes ANGUSTIFOLIA3 Gradient in Growing Leaves.

PubMed

Kawade, Kensuke; Tanimoto, Hirokazu; Horiguchi, Gorou; Tsukaya, Hirokazu

2017-09-05

The spatial gradient of signaling molecules is pivotal for establishing developmental patterns of multicellular organisms. It has long been proposed that these gradients could arise from the pure diffusion process of signaling molecules between cells, but whether this simplest mechanism establishes the formation of the tissue-scale gradient remains unclear. Plasmodesmata are unique channel structures in plants that connect neighboring cells for molecular transport. In this study, we measured cellular- and tissue-scale kinetics of molecular transport through plasmodesmata in Arabidopsis thaliana developing leaf primordia by fluorescence recovery assays. These trans-scale measurements revealed biophysical properties of diffusive molecular transport through plasmodesmata and revealed that the tissue-scale diffusivity, but not the cellular-scale diffusivity, is spatially different along the leaf proximal-to-distal axis. We found that the gradient in cell size along the developmental axis underlies this spatially different tissue-scale diffusivity. We then asked how this diffusion-based framework functions in establishing a signaling gradient of endogenous molecules. ANGUSTIFOLIA3 (AN3) is a transcriptional co-activator, and as we have shown here, it forms a long-range signaling gradient along the leaf proximal-to-distal axis to determine a cell-proliferation domain. By genetically engineering AN3 mobility, we assessed each contribution of cell-to-cell movement and tissue growth to the distribution of the AN3 gradient. We constructed a diffusion-based theoretical model using these quantitative data to analyze the AN3 gradient formation and demonstrated that it could be achieved solely by the diffusive molecular transport in a growing tissue. Our results indicate that the spatially different tissue-scale diffusivity is a core mechanism for AN3 gradient formation. This provides evidence that the pure diffusion process establishes the formation of the long-range signaling gradient in leaf development. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Coarse-grained molecular dynamics simulations for giant protein-DNA complexes

NASA Astrophysics Data System (ADS)

Takada, Shoji

Biomolecules are highly hierarchic and intrinsically flexible. Thus, computational modeling calls for multi-scale methodologies. We have been developing a coarse-grained biomolecular model where on-average 10-20 atoms are grouped into one coarse-grained (CG) particle. Interactions among CG particles are tuned based on atomistic interactions and the fluctuation matching algorithm. CG molecular dynamics methods enable us to simulate much longer time scale motions of much larger molecular systems than fully atomistic models. After broad sampling of structures with CG models, we can easily reconstruct atomistic models, from which one can continue conventional molecular dynamics simulations if desired. Here, we describe our CG modeling methodology for protein-DNA complexes, together with various biological applications, such as the DNA duplication initiation complex, model chromatins, and transcription factor dynamics on chromatin-like environment.
Multi-Scale Microstructural Thermoelectric Materials: Transport Behavior, Non-Equilibrium Preparation, and Applications.

PubMed

Su, Xianli; Wei, Ping; Li, Han; Liu, Wei; Yan, Yonggao; Li, Peng; Su, Chuqi; Xie, Changjun; Zhao, Wenyu; Zhai, Pengcheng; Zhang, Qingjie; Tang, Xinfeng; Uher, Ctirad

2017-05-01

Considering only about one third of the world's energy consumption is effectively utilized for functional uses, and the remaining is dissipated as waste heat, thermoelectric (TE) materials, which offer a direct and clean thermal-to-electric conversion pathway, have generated a tremendous worldwide interest. The last two decades have witnessed a remarkable development in TE materials. This Review summarizes the efforts devoted to the study of non-equilibrium synthesis of TE materials with multi-scale structures, their transport behavior, and areas of applications. Studies that work towards the ultimate goal of developing highly efficient TE materials possessing multi-scale architectures are highlighted, encompassing the optimization of TE performance via engineering the structures with different dimensional aspects spanning from the atomic and molecular scales, to nanometer sizes, and to the mesoscale. In consideration of the practical applications of high-performance TE materials, the non-equilibrium approaches offer a fast and controllable fabrication of multi-scale microstructures, and their scale up to industrial-size manufacturing is emphasized here. Finally, the design of two integrated power generating TE systems are described-a solar thermoelectric-photovoltaic hybrid system and a vehicle waste heat harvesting system-that represent perhaps the most important applications of thermoelectricity in the energy conversion area. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Nanoscale Bio-engineering Solutions for Space Exploration: The Nanopore Sequencer

NASA Technical Reports Server (NTRS)

Stolc, Viktor; Cozmuta, Ioana

2004-01-01

Characterization of biological systems at the molecular level and extraction of essential information for nano-engineering design to guide the nano-fabrication of solid-state sensors and molecular identification devices is a computational challenge. The alpha hemolysin protein ion channel is used as a model system for structural analysis of nucleic acids like DNA. Applied voltage draws a DNA strand and surrounding ionic solution through the biological nanopore. The subunits in the DNA strand block ion flow by differing amounts. Atomistic scale simulations are employed using NASA supercomputers to study DNA translocation, with the aim to enhance single DNA subunit identification. Compared to protein channels, solid-state nanopores offer a better temporal control of the translocation of DNA and the possibility to easily tune its chemistry to increase the signal resolution. Potential applications for NASA missions, besides real-time genome sequencing include astronaut health, life detection and decoding of various genomes.
Development of mass production technology for block copolymer lithographic materials

NASA Astrophysics Data System (ADS)

Himi, Toshiyuki; Matsuki, Ryota; Kosaka, Terumasa; Ogaki, Ryosuke; Kawaguchi, Yukio; Shimizu, Tetsuo

2017-03-01

We have successfully synthesized various and over wide range molecular weight block copolymers (BCPs): these are polystyrene(PS)-polymethylmethacrylate(PMMA) as general components and poly(4-trimethylsilylstyrene)(PTMSS)- poly(4-hydroxystyrene)(PHS) system as very strong segregated components (high chi) and multiblock type of those copolymers which form the microphase-separated structure pattern using living anionic polymerizing method by which the size of polymer can be precisely controlled. In addition, we were able to observe alternating lamellar and cylinder structures which were formed by our various BCPs using small angle X-ray scattering (SAXS). Moreover, we have successfully developed new apparatus for high volume manufacturing including our original technologies such as purification of monomer, improvement of wetted surface, and mechanical technology for high vacuum. And we have successfully synthesized all the BCPs with narrow molecular weight distribution (PDI <1.1) with large-scale apparatus.
The internal architecture of dendritic spines revealed by super-resolution imaging: What did we learn so far?

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacGillavry, Harold D., E-mail: h.d.macgillavry@uu.nl; Hoogenraad, Casper C., E-mail: c.hoogenraad@uu.nl

2015-07-15

The molecular architecture of dendritic spines defines the efficiency of signal transmission across excitatory synapses. It is therefore critical to understand the mechanisms that control the dynamic localization of the molecular constituents within spines. However, because of the small scale at which most processes within spines take place, conventional light microscopy techniques are not adequate to provide the necessary level of resolution. Recently, super-resolution imaging techniques have overcome the classical barrier imposed by the diffraction of light, and can now resolve the localization and dynamic behavior of proteins within small compartments with nanometer precision, revolutionizing the study of dendritic spinemore » architecture. Here, we highlight exciting new findings from recent super-resolution studies on neuronal spines, and discuss how these studies revealed important new insights into how protein complexes are assembled and how their dynamic behavior shapes the efficiency of synaptic transmission.« less
Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

NASA Astrophysics Data System (ADS)

Thubagere, Anupama J.; Thachuk, Chris; Berleant, Joseph; Johnson, Robert F.; Ardelean, Diana A.; Cherry, Kevin M.; Qian, Lulu

2017-02-01

Biochemical circuits made of rationally designed DNA molecules are proofs of concept for embedding control within complex molecular environments. They hold promise for transforming the current technologies in chemistry, biology, medicine and material science by introducing programmable and responsive behaviour to diverse molecular systems. As the transformative power of a technology depends on its accessibility, two main challenges are an automated design process and simple experimental procedures. Here we demonstrate the use of circuit design software, combined with the use of unpurified strands and simplified experimental procedures, for creating a complex DNA strand displacement circuit that consists of 78 distinct species. We develop a systematic procedure for overcoming the challenges involved in using unpurified DNA strands. We also develop a model that takes synthesis errors into consideration and semi-quantitatively reproduces the experimental data. Our methods now enable even novice researchers to successfully design and construct complex DNA strand displacement circuits.
Nanoscale Bioengineering Solutions for Space Exploration the Nanopore Sequencer

NASA Technical Reports Server (NTRS)

Ioana, Cozmuta; Viktor, Stoic

2005-01-01

Characterization of biological systems at the molecular level and extraction of essential information for nano-engineering design to guide the nano-fabrication of solid-state sensors and molecular identification devices is a computational challenge. The alpha hemolysin protein ion channel is used as a model system for structural analysis of nucleic acids like DNA. Applied voltage draws a DNA strand and surrounding ionic solution through the biological nanopore. The subunits in the DNA strand block ion flow by differing amounts. Atomistic scale simulations are employed using NASA supercomputers to study DNA translocation. with the aim to enhance single DNA subunit identification. Compared to protein channels, solid-state nanopores offer a better temporal control of the translocation of DNA and the possibility to easily tune its chemistry to increase the signal resolution. Potential applications for NASA missions, besides real-time genome sequencing include astronaut health, life detection and decoding of various genomes. http://phenomrph.arc.nasa.gov/index.php
Routing of individual polymers in designed patterns

NASA Astrophysics Data System (ADS)

Knudsen, Jakob Bach; Liu, Lei; Bank Kodal, Anne Louise; Madsen, Mikael; Li, Qiang; Song, Jie; Woehrstein, Johannes B.; Wickham, Shelley F. J.; Strauss, Maximilian T.; Schueder, Florian; Vinther, Jesper; Krissanaprasit, Abhichart; Gudnason, Daniel; Smith, Anton Allen Abbotsford; Ogaki, Ryosuke; Zelikin, Alexander N.; Besenbacher, Flemming; Birkedal, Victoria; Yin, Peng; Shih, William M.; Jungmann, Ralf; Dong, Mingdong; Gothelf, Kurt V.

2015-10-01

Synthetic polymers are ubiquitous in the modern world, but our ability to exert control over the molecular conformation of individual polymers is very limited. In particular, although the programmable self-assembly of oligonucleotides and proteins into artificial nanostructures has been demonstrated, we currently lack the tools to handle other types of synthetic polymers individually and thus the ability to utilize and study their single-molecule properties. Here we show that synthetic polymer wires containing short oligonucleotides that extend from each repeat can be made to assemble into arbitrary routings. The wires, which can be more than 200 nm in length, are soft and bendable, and the DNA strands allow individual polymers to self-assemble into predesigned routings on both two- and three-dimensional DNA origami templates. The polymers are conjugated and potentially conducting, and could therefore be used to create molecular-scale electronic or optical wires in arbitrary geometries.

Atomically precise edge chlorination of nanographenes and its application in graphene nanoribbons

PubMed Central

Tan, Yuan-Zhi; Yang, Bo; Parvez, Khaled; Narita, Akimitsu; Osella, Silvio; Beljonne, David; Feng, Xinliang; Müllen, Klaus

2013-01-01

Chemical functionalization is one of the most powerful and widely used strategies to control the properties of nanomaterials, particularly in the field of graphene. However, the ill-defined structure of the present functionalized graphene inhibits atomically precise structural characterization and structure-correlated property modulation. Here we present a general edge chlorination protocol for atomically precise functionalization of nanographenes at different scales from 1.2 to 3.4 nm and its application in graphene nanoribbons. The well-defined edge chlorination is unambiguously confirmed by X-ray single-crystal analysis, which also discloses the characteristic non-planar molecular shape and detailed bond lengths of chlorinated nanographenes. Chlorinated nanographenes and graphene nanoribbons manifest enhanced solution processability associated with decreases in the optical band gap and frontier molecular orbital energy levels, exemplifying the structure-correlated property modulation by precise edge chlorination. PMID:24212200
Perfect mixing of immiscible macromolecules at fluid interfaces

NASA Astrophysics Data System (ADS)

Sheiko, Sergei; Matyjaszewski, Krzysztof; Tsukruk, Vladimir; Carrillo, Jan-Michael; Rubinstein, Michael; Dobrynin, Andrey; Zhou, Jing

2014-03-01

Macromolecules typically phase separate unless their shapes and chemical compositions are tailored to explicitly drive mixing. But now our research has shown that physical constraints can drive spontaneous mixing of chemically different species. We have obtained long-range 2D arrays of perfectly mixed macromolecules having a variety of molecular architectures and chemistries, including linear chains, block-copolymer stars, and bottlebrush copolymers with hydrophobic, hydrophilic, and lipophobic chemical compositions. This is achieved by entropy-driven enhancement of steric repulsion between macromolecules anchored on a substrate. By monitoring the kinetics of mixing, we have proved that molecular intercalation is an equilibrium state. The array spacing is controlled by the length of the brush side chains. This entropic templating strategy opens new ways for generating patterns on sub-100 nm length scales with potential application in lithography, directed self-assembly, and biomedical assays. Financial support from the National Science Foundation DMR-0906985, DMR-1004576, DMR-1122483, and DMR-0907515.
Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport.

PubMed

Howard, Rebecca J; Carnevale, Vincenzo; Delemotte, Lucie; Hellmich, Ute A; Rothberg, Brad S

2018-04-01

Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.
Catalyst Residence Time Distributions in Riser Reactors for Catalytic Fast Pyrolysis. Part 2: Pilot-Scale Simulations and Operational Parameter Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foust, Thomas D.; Ziegler, Jack L.; Pannala, Sreekanth

2017-02-21

Here, wsing the validated simulation model developed in part one of this study for biomass catalytic fast pyrolysis (CFP), we assess the functional utility of using this validated model to assist in the development of CFP processes in fluidized catalytic cracking (FCC) reactors to a commercially viable state. Specifically, we examine the effects of mass flow rates, boundary conditions (BCs), pyrolysis vapor molecular weight variation, and the impact of the chemical cracking kinetics on the catalyst residence times. The factors that had the largest impact on the catalyst residence time included the feed stock molecular weight and the degree ofmore » chemical cracking as controlled by the catalyst activity. Lastly, because FCC reactors have primarily been developed and utilized for petroleum cracking, we perform a comparison analysis of CFP with petroleum and show the operating regimes are fundamentally different.« less
Reviews and syntheses: Four decades of modeling methane cycling in terrestrial ecosystems

DOE PAGES

Xu, Xiaofeng; Yuan, Fengming; Hanson, Paul J.; ...

2016-01-28

A number of numerical models have been developed to quantify the magnitude, over the past 4 decades, such that we have investigated the spatial and temporal variations, and understand the underlying mechanisms and environmental controls of methane (CH 4) fluxes within terrestrial ecosystems. These CH 4 models are also used for integrating multi-scale CH 4 data, such as laboratory-based incubation and molecular analysis, field observational experiments, remote sensing, and aircraft-based measurements across a variety of terrestrial ecosystems. Here we summarize 40 terrestrial CH 4 models to characterize their strengths and weaknesses and to suggest a roadmap for future model improvementmore » and application. Our key findings are that (1) the focus of CH 4 models has shifted from theoretical to site- and regional-level applications over the past 4 decades, (2) large discrepancies exist among models in terms of representing CH 4 processes and their environmental controls, and (3) significant data–model and model–model mismatches are partially attributed to different representations of landscape characterization and inundation dynamics. Furthermore three areas for future improvements and applications of terrestrial CH 4 models are that (1) CH 4 models should more explicitly represent the mechanisms underlying land–atmosphere CH 4 exchange, with an emphasis on improving and validating individual CH 4 processes over depth and horizontal space, (2) models should be developed that are capable of simulating CH 4 emissions across highly heterogeneous spatial and temporal scales, particularly hot moments and hotspots, and (3) efforts should be invested to develop model benchmarking frameworks that can easily be used for model improvement, evaluation, and integration with data from molecular to global scales. Finally, these improvements in CH 4 models would be beneficial for the Earth system models and further simulation of climate–carbon cycle feedbacks.« less
Modeling material interfaces with hybrid adhesion method

DOE PAGES

Brown, Nicholas Taylor; Qu, Jianmin; Martinez, Enrique

2017-01-27

A molecular dynamics simulation approach is presented to approximate layered material structures using discrete interatomic potentials through classical mechanics and the underlying principles of quantum mechanics. This method isolates the energetic contributions of the system into two pure material layers and an interfacial region used to simulate the adhesive properties of the diffused interface. The strength relationship of the adhesion contribution is calculated through small-scale separation calculations and applied to the molecular surfaces through an inter-layer bond criterion. By segregating the contributions into three regions and accounting for the interfacial excess energies through the adhesive surface bonds, it is possiblemore » to model each material with an independent potential while maintaining an acceptable level of accuracy in the calculation of mechanical properties. This method is intended for the atomistic study of the delamination mechanics, typically observed in thin-film applications. Therefore, the work presented in this paper focuses on mechanical tensile behaviors, with observations in the elastic modulus and the delamination failure mode. To introduce the hybrid adhesion method, we apply the approach to an ideal bulk copper sample, where an interface is created by disassociating the force potential in the middle of the structure. Various mechanical behaviors are compared to a standard EAM control model to demonstrate the adequacy of this approach in a simple setting. In addition, we demonstrate the robustness of this approach by applying it on (1) a Cu-Cu 2O interface with interactions between two atom types, and (2) an Al-Cu interface with two dissimilar FCC lattices. These additional examples are verified against EAM and COMB control models to demonstrate the accurate simulation of failure through delamination, and the formation and propagation of dislocations under loads. Finally, the results conclude that by modeling the energy contributions of an interface using hybrid adhesion bonds, we can provide an accurate approximation method for studies of large-scale mechanical properties, as well as the representation of various delamination phenomena at the atomic scale.« less
Functional Nanostructured Materials Based on Polymerized Surfactant Liquid Crystal Assemblies Liquid Crystal Assemblies

NASA Astrophysics Data System (ADS)

Gin, Douglas

2003-03-01

The development of materials with controlled nanostructures is one of the most important new areas of scientific research in chemistry and engineering. Our research group has developed a novel approach for making nanostructured polymer materials with unique functional properties using liquid crystals as starting materials. In this approach, we design polymerizable organic building blocks based on lyotropic liquid crystals (LLCs) (i.e., amphiphiles or surfactants) that carry, or can accommodate, a functional property of general interest. Through appropriate molecular design, these monomers self-assemble in the presence of water into fluid, yet ordered phase-separated, water-hydrocarbon assemblies with predictable nanoscale geometries. The architectures of these LLC phases can range from stacked two-dimensional lamellae to hexagonally ordered cylindrical channels with uniform feature sizes in the 1-10 nm range. These LLC phases are then photopolymerized into robust polymer networks with preservation of their small-scale structures. This approach allows us to investigate the effect of nanometer-scale architecture on important bulk properties, as well as to engineer chemical environments on the nanometer-scale for several areas of application. In this talk, new functional materials based on the polymerization of the lyotropic inverted hexagonal phase will be presented as one example of our general approach. Issues in the design and photopolymerization of functional amphiphilic monomers that adopt this LC architecture will be discussed. More importantly, the use of the resulting nanostructured polymer networks in three areas of application will be presented: (1) as templates for the synthesis of functional nanocomposites; (2) as tunable heterogeneous catalysts, and (3) as nanoporous membrane and separation media. In particular, issues pertaining to the contribution of nanoscale architecture to the performance of these systems will be highlighted. Opportunities for tailoring the nanoscale chemical environment and architecture of these materials through molecular design will be presented. Finally, the development of methods for controlling macroscopic orientation through processing will also be discussed.
Modelling of electrokinetic phenomena involving confined polymers: Applications to DNA separation and electroosmotic flow control

NASA Astrophysics Data System (ADS)

Tessier, Frederic

Microfluidic and nanofluidic technology is revolutionizing experimental practices in analytical chemistry, molecular biology and medicine. Indeed, the development of systems of small dimensions for the processing of fluids heralds the miniaturization of traditional, cumbersome laboratory equipment onto robust, portable and efficient microchip devices (similar to the electronic microchips found in computers). Moreover, the conjunction of scale between the smallest man-made device and the largest macromolecules evolved by Nature is fertile ground for the blooming of our knowledge about the key processes of life. In fact, the conjunction is threefold, because modern computational resources also allow us to contemplate a rather explicit modelling of physical systems between the nanoscale and the microscale. In the five articles comprising this thesis, we present the results of computer simulations that address specific questions concerning the operation of two different model systems relevant to the development of small-scale fluidic devices for the manipulation and analysis of biomolecules. First, we use a Bond-Fluctuation Monte Carlo approach to study the electrophoretic drift of macromolecules across an entropic trap array built for the length separation of long, double-stranded DNA molecules. We show that the motion of the molecules is consistent with a simple balance between electric and entropic forces, in terms of a single characteristic parameter. We also extract detailed information on polymer deformation during migration, predict the separation of topoisomers, and investigate innovative ratchet driving regimes. Secondly, we present theoretical derivations, numerical calculations and Molecular Dynamics simulation results for an electrolyte confined in a capillary of nanoscopic dimensions. In particular, we study the effectiveness of neutral grafted polymer chains in reducing the magnitude of electroosmotic flow (fluid flow induced by an external electric field). Our results constitute the first independent, quantitative verification of theoretical scaling predictions for the coupling between grafted macromolecules and electroosmotic flow. Such simulations will contribute to the rationalization of the existing empirical knowledge about flow control with polymer coatings.
A unique skeletal microstructure of the deep-sea micrabaciid scleractinian corals

NASA Astrophysics Data System (ADS)

Janiszewska, Katarzyna; Stolarski, Jaroslaw; Benzerara, Karim; Meibom, Anders; Mazur, Maciej; Kitahara, Marcelo; Cairns, Stephen D.

2010-05-01

Structural and biogeochemical properties of the skeleton of many invertebrates rely on organic matrix-mediated biomineralization processes. Organic matrices, composed of complex assemblages of macromolecules (proteins, polysaccharides), may control nucleation, spatial delineation and organization of basic microstructural units. Biologically controlled mineralization is also suggested for the scleractinian corals whose different, molecularly recognized clades are supported by distinct types of skeletal microstructures. Main differences in scleractinian coral skeletal microstructures suggested so far consist in (1) varying spatial relationships between Rapid Accretion Deposits (RAD, 'centers of calcification') and thickening deposits (TD, 'fibers'), and (2) varying arrangements of biomineral fibers into higher order structures (e.g., bundles of fibers perpendicular to skeletal surfaces in some 'caryophylliid' corals vs. scale-like units with fibers parallel to the surface in acroporiids). However, a common feature of biomineral fibers in corals described thus far was their similar crystallographic arrangement within larger meso-scale structures (bundles of fibers) and continuity between successive growth layers. Herein we show that representatives of the deep-sea scleractinian family Micrabaciidae (genera: Letepsammia, Rhombopsammia, Stephanophyllia, Leptopenus) have thickening deposits composed of irregular meshwork of short (1-2 μm) and extremely thin (ca. 100-300 nm) fibers organized into small bundles (ca. 1-2 μm thick). Longer axes of fibers are aligned within individual bundles that, in turn, show rather irregular arrangement on the growing surfaces and within the skeleton (irregular criss-cross pattern). In contrast to other scleractinians (including deep-water 'caryophylliids', fungiacyathids, and anthemiphyllids sympatric with micrabaciids), growth layers are not distinct. Also the regions of rapid accretion and thickening deposits are not clearly separated at the meso-scale. However, AFM and FESEM observations of RAD show nanogranular units (ca. 30-100 nm in diameter) typical of fast growing skeletal regions. Unique microstructural organization of the micrabaciid skeleton supports their monophyletic status (reinforced by macromorphological and molecular data), and points to a diversity of organic matrix-mediated biomineralization strategies in Scleractinia.
Outcome of Molecular Targeted Agents Plus Chemotherapy for Second-Line Therapy of Metastatic Colorectal Cancer: A Meta-Analysis of Randomized Trials.

PubMed

Pei, Xueqing; Liu, Yu; Sun, Liwei; Zhang, Jun; Fang, Yuanyuan; Liao, Xin; Liu, Jian; Zhang, Cuntai; Yin, Tiejun

2016-12-01

The aim of this study was to evaluate the efficacy and toxicity of molecular targeted agents plus chemotherapy compared with chemotherapy alone as second-line therapy for patients with metastatic colorectal cancer (mCRC). We identified randomized controlled trials that compared molecular targeted agents plus chemotherapy with chemotherapy alone by searching the PubMed and Embase databases for articles published between January 2000 and September 2015. The outcome measures included progression-free survival, overall survival, objective response rate, and adverse events. Two investigators independently performed the information retrieval, screening, and data extraction. Stata 10.0 software was used to statistically analyze the extracted data. In accordance with our inclusion criteria, 11 trials, with a total of 7440 patients, were included in this meta-analysis through rounds of selection. We divided the biologic agents used into 3 subgroups based on the type of biologic agents-vascular endothelial growth factor (VEGF) inhibitor, epidermal growth factor receptor inhibitor, and other pathway inhibitors. Our results suggested that the regimen of a molecular targeted agent plus chemotherapy had a significant advantage in progression-free survival, overall survival, and objective response rate over chemotherapy alone (hazard ratio, 0.74; 95% confidence interval [CI], 0.70-0.78; hazard ratio, 0.88; 95% CI, 0.83-0.93; risk ratio, 2.24; 95% CI: 1.58-3.17, respectively). However, the rate of grade ≥ 3 adverse events was also higher in the combination therapy arm (risk ratio, 1.25; 95% CI, 1.17-1.33). Subgroup analysis showed that the combination of VEGF inhibitor with chemotherapy had a significant advantage in PFS, OS, and ORR over chemotherapy alone, but there was also a higher risk ratio in adverse events for this combination compared with the control group. In conclusion, a molecular targeted agent, especially VEGF inhibitor, plus chemotherapy is a worthwhile combination for patients with metastatic colorectal cancer as second-line therapy. However, more randomized controlled trials on a larger scale are needed for evaluating the value of epidermal growth factor receptor and other pathway inhibitors. Copyright Â© 2016 Elsevier Inc. All rights reserved.
TRIGGERED STAR FORMATION SURROUNDING WOLF-RAYET STAR HD 211853

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu Tie; Wu Yuefang; Zhang Huawei

The environment surrounding Wolf-Rayet (W-R) star HD 211853 is studied in molecular, infrared, as well as radio, and H I emission. The molecular ring consists of well-separated cores, which have a volume density of 10{sup 3} cm{sup -3} and kinematic temperature {approx}20 K. Most of the cores are under gravitational collapse due to external pressure from the surrounding ionized gas. From the spectral energy distribution modeling toward the young stellar objects, the sequential star formation is revealed on a large scale in space spreading from the W-R star to the molecular ring. A small-scale sequential star formation is revealed towardmore » core 'A', which harbors a very young star cluster. Triggered star formations are thus suggested. The presence of the photodissociation region, the fragmentation of the molecular ring, the collapse of the cores, and the large-scale sequential star formation indicate that the 'collect and collapse' process functions in this region. The star-forming activities in core 'A' seem to be affected by the 'radiation-driven implosion' process.« less
Direct observation of molecular cooperativity near the glass transition.

PubMed

Russell, E V; Israeloff, N E

2000-12-07

The increasingly sluggish response of a supercooled liquid as it nears its glass transition (for example, refrigerated honey) is prototypical of glassy dynamics found in proteins, neural networks and superconductors. The notion that molecules rearrange cooperatively has long been postulated to explain diverging relaxation times and broadened (non-exponential) response functions near the glass transition. Recently, cooperativity was observed and analysed in colloid glasses and in simulations of binary liquids well above the glass transition. But nanometre-scale studies of cooperativity at the molecular glass transition are lacking. Important issues to be resolved include the precise form of the cooperativity and its length scale, and whether the broadened response is intrinsic to individual cooperative regions, or arises only from heterogeneity in an ensemble of such regions. Here we describe direct observations of molecular cooperativity near the glass transition in polyvinylacetate (PVAc), using nanometre-scale probing of dielectric fluctuations. Molecular clusters switched spontaneously among two to four distinct configurations, producing random telegraph noise. Our analysis of these noise signals and their power spectra reveals that individual clusters exhibit transient dynamical heterogeneity and non-exponential kinetics.
Computational Nanotechnology of Molecular Materials, Electronics, and Actuators with Carbon Nanotubes and Fullerenes

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Menon, Madhu; Cho, Kyeongjae; Biegel, Bryan (Technical Monitor)

2001-01-01

The role of computational nanotechnology in developing next generation of multifunctional materials, molecular scale electronic and computing devices, sensors, actuators, and machines is described through a brief review of enabling computational techniques and few recent examples derived from computer simulations of carbon nanotube based molecular nanotechnology.
Statistical Inference for Big Data Problems in Molecular Biophysics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramanathan, Arvind; Savol, Andrej; Burger, Virginia

2012-01-01

We highlight the role of statistical inference techniques in providing biological insights from analyzing long time-scale molecular simulation data. Technologi- cal and algorithmic improvements in computation have brought molecular simu- lations to the forefront of techniques applied to investigating the basis of living systems. While these longer simulations, increasingly complex reaching petabyte scales presently, promise a detailed view into microscopic behavior, teasing out the important information has now become a true challenge on its own. Mining this data for important patterns is critical to automating therapeutic intervention discovery, improving protein design, and fundamentally understanding the mech- anistic basis of cellularmore » homeostasis.« less
Experimental design and quantitative analysis of microbial community multiomics.

PubMed

Mallick, Himel; Ma, Siyuan; Franzosa, Eric A; Vatanen, Tommi; Morgan, Xochitl C; Huttenhower, Curtis

2017-11-30

Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed. Here, we survey current best practices for experimental design in microbiome molecular epidemiology, including technologies for generating, analyzing, and integrating microbiome multiomics data. We highlight studies that have identified molecular bioactives that influence human health, and we suggest steps for scaling translational microbiome research to high-throughput target discovery across large populations.
Influence of macromolecular architecture on necking in polymer extrusion film casting process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pol, Harshawardhan; Banik, Sourya; Azad, Lal Busher

2015-05-22

Extrusion film casting (EFC) is an important polymer processing technique that is used to produce several thousand tons of polymer films/coatings on an industrial scale. In this research, we are interested in understanding quantitatively how macromolecular chain architecture (for example long chain branching (LCB) or molecular weight distribution (MWD or PDI)) influences the necking and thickness distribution of extrusion cast films. We have used different polymer resins of linear and branched molecular architecture to produce extrusion cast films under controlled experimental conditions. The necking profiles of the films were imaged and the velocity profiles during EFC were monitored using particlemore » tracking velocimetry (PTV) technique. Additionally, the temperature profiles were captured using an IR thermography and thickness profiles were calculated. The experimental results are compared with predictions of one-dimensional flow model of Silagy et al{sup 1} wherein the polymer resin rheology is modeled using molecular constitutive equations such as the Rolie-Poly (RP) and extended Pom Pom (XPP). We demonstrate that the 1-D flow model containing the molecular constitutive equations provides new insights into the role of macromolecular chain architecture on film necking.{sup 1}D. Silagy, Y. Demay, and J-F. Agassant, Polym. Eng. Sci., 36, 2614 (1996)« less
Molecular Dynamics of the Proline Switch and Its Role in Crk Signaling

PubMed Central

2015-01-01

The Crk adaptor proteins play a central role as a molecular timer for the formation of protein complexes including various growth and differentiation factors. The loss of regulation of Crk results in many kinds of cancers. A self-regulatory mechanism for Crk was recently proposed, which involves domain–domain rearrangement. It is initiated by a cis–trans isomerization of a specific proline residue (Pro238 in chicken Crk II) and can be accelerated by Cyclophilin A. To understand how the proline switch controls the autoinhibition at the molecular level, we performed large-scale molecular dynamics and metadynamics simulations in the context of short peptides and multidomain constructs of chicken Crk II. We found that the equilibrium and kinetic properties of the macrostates are regulated not only by the local environments of specified prolines but also by the global organization of multiple domains. We observe the two macrostates (cis closed/autoinhibited and trans open/uninhibited) consistent with NMR experiments and predict barriers. We also propose an intermediate state, the trans closed state, which interestingly was reported to be a prevalent state in human Crk II. The existence of this macrostate suggests that the rate of switching off the autoinhibition by Cyp A may be limited by the relaxation rate of this intermediate state. PMID:24702481
Molecular dynamics of the proline switch and its role in Crk signaling.

PubMed

Xia, Junchao; Levy, Ronald M

2014-05-01

The Crk adaptor proteins play a central role as a molecular timer for the formation of protein complexes including various growth and differentiation factors. The loss of regulation of Crk results in many kinds of cancers. A self-regulatory mechanism for Crk was recently proposed, which involves domain-domain rearrangement. It is initiated by a cis-trans isomerization of a specific proline residue (Pro238 in chicken Crk II) and can be accelerated by Cyclophilin A. To understand how the proline switch controls the autoinhibition at the molecular level, we performed large-scale molecular dynamics and metadynamics simulations in the context of short peptides and multidomain constructs of chicken Crk II. We found that the equilibrium and kinetic properties of the macrostates are regulated not only by the local environments of specified prolines but also by the global organization of multiple domains. We observe the two macrostates (cis closed/autoinhibited and trans open/uninhibited) consistent with NMR experiments and predict barriers. We also propose an intermediate state, the trans closed state, which interestingly was reported to be a prevalent state in human Crk II. The existence of this macrostate suggests that the rate of switching off the autoinhibition by Cyp A may be limited by the relaxation rate of this intermediate state.
WE-DE-202-02: Are Track Structure Simulations Truly Needed for Radiobiology at the Cellular and Tissue Levels?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stewart, R.

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are themore » most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)« less
WE-DE-202-00: Connecting Radiation Physics with Computational Biology

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are themore » most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)« less

Atomistic simulations of materials: Methods for accurate potentials and realistic time scales

NASA Astrophysics Data System (ADS)

Tiwary, Pratyush

This thesis deals with achieving more realistic atomistic simulations of materials, by developing accurate and robust force-fields, and algorithms for practical time scales. I develop a formalism for generating interatomic potentials for simulating atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high-energy collisions. This is done by fitting against an extensive database of ab initio results, as well as to experimental measurements for mixed oxide nuclear fuels. The applicability of these interactions to a variety of mixed environments beyond the fitting domain is also assessed. The employed formalism makes these potentials applicable across all interatomic distances without the need for any ambiguous splining to the well-established short-range Ziegler-Biersack-Littmark universal pair potential. We expect these to be reliable potentials for carrying out damage simulations (and molecular dynamics simulations in general) in nuclear fuels of varying compositions for all relevant atomic collision energies. A hybrid stochastic and deterministic algorithm is proposed that while maintaining fully atomistic resolution, allows one to achieve milliseconds and longer time scales for several thousands of atoms. The method exploits the rare event nature of the dynamics like other such methods, but goes beyond them by (i) not having to pick a scheme for biasing the energy landscape, (ii) providing control on the accuracy of the boosted time scale, (iii) not assuming any harmonic transition state theory (HTST), and (iv) not having to identify collective coordinates or interesting degrees of freedom. The method is validated by calculating diffusion constants for vacancy-mediated diffusion in iron metal at low temperatures, and comparing against brute-force high temperature molecular dynamics. We also calculate diffusion constants for vacancy diffusion in tantalum metal, where we compare against low-temperature HTST as well. The robustness of the algorithm with respect to the only free parameter it involves is ascertained. The method is then applied to perform tensile tests on gold nanopillars on strain rates as low as 100/s, bringing out the perils of high strain-rate molecular dynamics calculations. We also calculate temperature and stress dependence of activation free energy for surface nucleation of dislocations in pristine gold nanopillars under realistic loads. While maintaining fully atomistic resolution, we reach the fraction-of-a-second time scale regime. It is found that the activation free energy depends significantly and nonlinearly on the driving force (stress or strain) and temperature, leading to very high activation entropies for surface dislocation nucleation.
DOE Office of Scientific and Technical Information (OSTI.GOV)

McMahon, S.

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are themore » most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)« less
WE-DE-202-01: Connecting Nanoscale Physics to Initial DNA Damage Through Track Structure Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schuemann, J.

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are themore » most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological processes are too complex for a mechanistic approach. Can computer simulations be used to guide future biological research? We will debate the feasibility of explaining biology from a physicists’ perspective. Learning Objectives: Understand the potential applications and limitations of computational methods for dose-response modeling at the molecular, cellular and tissue levels Learn about mechanism of action underlying the induction, repair and biological processing of damage to DNA and other constituents Understand how effects and processes at one biological scale impact on biological processes and outcomes on other scales J. Schuemann, NCI/NIH grantsS. McMahon, Funding: European Commission FP7 (grant EC FP7 MC-IOF-623630)« less
Mechanobiology of Platelets: Techniques to Study the Role of Fluid Flow and Platelet Retraction Forces at the Micro- and Nano-Scale

PubMed Central

Feghhi, Shirin; Sniadecki, Nathan J.

2011-01-01

Coagulation involves a complex set of events that are important in maintaining hemostasis. Biochemical interactions are classically known to regulate the hemostatic process, but recent evidence has revealed that mechanical interactions between platelets and their surroundings can also play a substantial role. Investigations into platelet mechanobiology have been challenging however, due to the small dimensions of platelets and their glycoprotein receptors. Platelet researchers have recently turned to microfabricated devices to control these physical, nanometer-scale interactions with a higher degree of precision. These approaches have enabled exciting, new insights into the molecular and biomechanical factors that affect platelets in clot formation. In this review, we highlight the new tools used to understand platelet mechanobiology and the roles of adhesion, shear flow, and retraction forces in clot formation. PMID:22272117
Time-dependent Schrödinger equation for molecular core-hole dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Picón, A.

2017-02-01

X-ray spectroscopy is an important tool for the investigation of matter. X rays primarily interact with inner-shell electrons, creating core (inner-shell) holes that will decay on the time scale of attoseconds to a few femtoseconds through electron relaxations involving the emission of a photon or an electron. Furthermore, the advent of femtosecond x-ray pulses expands x-ray spectroscopy to the time domain and will eventually allow the control of core-hole population on time scales comparable to core-vacancy lifetimes. For both cases, a theoretical approach that accounts for the x-ray interaction while the electron relaxations occur is required. We describe a time-dependentmore » framework, based on solving the time-dependent Schrödinger equation, that is suitable for describing the induced electron and nuclear dynamics.« less
Extremely small bandgaps, engineered by controlled multi-scale ordering in InAsSb

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sarney, W. L.; Svensson, S. P.; Lin, Y.

2016-06-07

The relationship between the effective bandgap and the crystalline structure in ordered InAsSb material has been studied. Modulation of the As/Sb ratio was induced along the growth direction during molecular beam epitaxy, producing a strained layer superlattice. To enable the use of concentration ratios near unity in both layers in the period, the structures were grown with negligible net strain on a virtual substrate with a lattice constant considerably larger than that of GaSb. The bandgap line-up of InAsSb layers with different compositions is such that a type II superlattice is formed, which exhibits smaller bandgaps than either of themore » two constituents. It can also be smaller than the possible minimum direct-bandgap of the alloy. From observations of CuPt ordering in bulk layers with small amounts of strain of both signs, we postulate that strain is the main driving force for atomic ordering in InAsSb. Because the modulated structures exhibit small but opposing amounts of strain, both layers in the period exhibit ordering at the atomic scale throughout the structure. Since the strain can be controlled, the ordering can be controlled and sustained for arbitrary thick layers, unlike the situation in uniform bulk layers where the residual strain eventually leads to dislocation formation. This offers a unique way of using ordering at two different scales to engineer the band-structure.« less
Multi-scale theory-assisted nano-engineering of plasmonic-organic hybrid electro-optic device performance

NASA Astrophysics Data System (ADS)

Elder, Delwin L.; Johnson, Lewis E.; Tillack, Andreas F.; Robinson, Bruce H.; Haffner, Christian; Heni, Wolfgang; Hoessbacher, Claudia; Fedoryshyn, Yuriy; Salamin, Yannick; Baeuerle, Benedikt; Josten, Arne; Ayata, Masafumi; Koch, Ueli; Leuthold, Juerg; Dalton, Larry R.

2018-02-01

Multi-scale (correlated quantum and statistical mechanics) modeling methods have been advanced and employed to guide the improvement of organic electro-optic (OEO) materials, including by analyzing electric field poling induced electro-optic activity in nanoscopic plasmonic-organic hybrid (POH) waveguide devices. The analysis of in-device electro-optic activity emphasizes the importance of considering both the details of intermolecular interactions within organic electro-optic materials and interactions at interfaces between OEO materials and device architectures. Dramatic improvement in electro-optic device performance-including voltage-length performance, bandwidth, energy efficiency, and lower optical losses have been realized. These improvements are critical to applications in telecommunications, computing, sensor technology, and metrology. Multi-scale modeling methods illustrate the complexity of improving the electro-optic activity of organic materials, including the necessity of considering the trade-off between improving poling-induced acentric order through chromophore modification and the reduction of chromophore number density associated with such modification. Computational simulations also emphasize the importance of developing chromophore modifications that serve multiple purposes including matrix hardening for enhanced thermal and photochemical stability, control of matrix dimensionality, influence on material viscoelasticity, improvement of chromophore molecular hyperpolarizability, control of material dielectric permittivity and index of refraction properties, and control of material conductance. Consideration of new device architectures is critical to the implementation of chipscale integration of electronics and photonics and achieving the high bandwidths for applications such as next generation (e.g., 5G) telecommunications.
From crater functions to partial differential equations: a new approach to ion bombardment induced nonequilibrium pattern formation.

PubMed

Norris, Scott A; Brenner, Michael P; Aziz, Michael J

2009-06-03

We develop a methodology for deriving continuum partial differential equations for the evolution of large-scale surface morphology directly from molecular dynamics simulations of the craters formed from individual ion impacts. Our formalism relies on the separation between the length scale of ion impact and the characteristic scale of pattern formation, and expresses the surface evolution in terms of the moments of the crater function. We demonstrate that the formalism reproduces the classical Bradley-Harper results, as well as ballistic atomic drift, under the appropriate simplifying assumptions. Given an actual set of converged molecular dynamics moments and their derivatives with respect to the incidence angle, our approach can be applied directly to predict the presence and absence of surface morphological instabilities. This analysis represents the first work systematically connecting molecular dynamics simulations of ion bombardment to partial differential equations that govern topographic pattern-forming instabilities.
Progress toward bridging from atomistic to continuum modeling to predict nuclear waste glass dissolution.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zapol, Peter; Bourg, Ian; Criscenti, Louise Jacqueline

2011-10-01

This report summarizes research performed for the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Subcontinuum and Upscaling Task. The work conducted focused on developing a roadmap to include molecular scale, mechanistic information in continuum-scale models of nuclear waste glass dissolution. This information is derived from molecular-scale modeling efforts that are validated through comparison with experimental data. In addition to developing a master plan to incorporate a subcontinuum mechanistic understanding of glass dissolution into continuum models, methods were developed to generate constitutive dissolution rate expressions from quantum calculations, force field models were selected to generate multicomponent glass structures and gel layers,more » classical molecular modeling was used to study diffusion through nanopores analogous to those in the interfacial gel layer, and a micro-continuum model (K{mu}C) was developed to study coupled diffusion and reaction at the glass-gel-solution interface.« less
W49A: A Massive Molecular Cloud Forming a Massive Star Cluster in the Galactic Disk

NASA Astrophysics Data System (ADS)

Galvan-Madrid, Roberto; Liu, Hauyu Baobab; Pineda, Jaime E.; Zhang, Zhi-Yu; Ginsburg, Adam; Roman-Zuñiga, Carlos; Peters, Thomas

2015-08-01

I summarize our current results of the MUSCLE survey of W49A, the most luminous star formation region in the Milky Way. Our approach emphasizes multi-scale, multi-resolution imaging in dust, ionized-, and molecular gas, to trace the multiple gas components from <0.1 pc (core scale) all the way up to the scale of the entire giant molecular cloud (GMC), ˜100 pc. The 106 M⊙ GMC is structured in a radial network of filaments that converges toward the central 'hub' with ˜2x105 M⊙, which contains within a few pc a deeply embedded young massive cluster (YMC) of stellar mass ~5x104 M⊙. We also discuss the dynamics of the filamentary network, the role of turbulence in the formation of this YMC, and how objects like W49A can link Milky Way and extragalactic star formation relations.
Light microscopy applications in systems biology: opportunities and challenges

PubMed Central

2013-01-01

Biological systems present multiple scales of complexity, ranging from molecules to entire populations. Light microscopy is one of the least invasive techniques used to access information from various biological scales in living cells. The combination of molecular biology and imaging provides a bottom-up tool for direct insight into how molecular processes work on a cellular scale. However, imaging can also be used as a top-down approach to study the behavior of a system without detailed prior knowledge about its underlying molecular mechanisms. In this review, we highlight the recent developments on microscopy-based systems analyses and discuss the complementary opportunities and different challenges with high-content screening and high-throughput imaging. Furthermore, we provide a comprehensive overview of the available platforms that can be used for image analysis, which enable community-driven efforts in the development of image-based systems biology. PMID:23578051
The alignment of molecular cloud magnetic fields with the spiral arms in M33.

PubMed

Li, Hua-bai; Henning, Thomas

2011-11-16

The formation of molecular clouds, which serve as stellar nurseries in galaxies, is poorly understood. A class of cloud formation models suggests that a large-scale galactic magnetic field is irrelevant at the scale of individual clouds, because the turbulence and rotation of a cloud may randomize the orientation of its magnetic field. Alternatively, galactic fields could be strong enough to impose their direction upon individual clouds, thereby regulating cloud accumulation and fragmentation, and affecting the rate and efficiency of star formation. Our location in the disk of the Galaxy makes an assessment of the situation difficult. Here we report observations of the magnetic field orientation of six giant molecular cloud complexes in the nearby, almost face-on, galaxy M33. The fields are aligned with the spiral arms, suggesting that the large-scale field in M33 anchors the clouds. ©2011 Macmillan Publishers Limited. All rights reserved
A stochastic thermostat algorithm for coarse-grained thermomechanical modeling of large-scale soft matters: Theory and application to microfilaments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Tong; Gu, YuanTong, E-mail: yuantong.gu@qut.edu.au

As all-atom molecular dynamics method is limited by its enormous computational cost, various coarse-grained strategies have been developed to extend the length scale of soft matters in the modeling of mechanical behaviors. However, the classical thermostat algorithm in highly coarse-grained molecular dynamics method would underestimate the thermodynamic behaviors of soft matters (e.g. microfilaments in cells), which can weaken the ability of materials to overcome local energy traps in granular modeling. Based on all-atom molecular dynamics modeling of microfilament fragments (G-actin clusters), a new stochastic thermostat algorithm is developed to retain the representation of thermodynamic properties of microfilaments at extra coarse-grainedmore » level. The accuracy of this stochastic thermostat algorithm is validated by all-atom MD simulation. This new stochastic thermostat algorithm provides an efficient way to investigate the thermomechanical properties of large-scale soft matters.« less
Nanoscopic length scale dependence of hydrogen bonded molecular associates’ dynamics in methanol

PubMed Central

Bertrand, C. E.; Self, J. L.; Copley, J. R. D.; Faraone, A.

2017-01-01

In a recent paper [C. E. Bertrand et al., J. Chem. Phys. 145, 014502 (2016)], we have shown that the collective dynamics of methanol shows a fast relaxation process related to the standard density-fluctuation heat mode and a slow non-Fickian mode originating from the hydrogen bonded molecular associates. Here we report on the length scale dependence of this slow relaxation process. Using quasielastic neutron scattering and molecular dynamics simulations, we show that the dynamics of the slow process is affected by the structuring of the associates, which is accessible through polarized neutron diffraction experiments. Using a series of partially deuterated samples, the dynamics of the associates is investigated and is found to have a similar time scale to the lifetime of hydrogen bonding in the system. Both the structural relaxation and the dynamics of the associates are thermally activated by the breaking of hydrogen bonding. PMID:28527447
Solvation of fluoro-acetonitrile in water by 2D-IR spectroscopy: A combined experimental-computational study

NASA Astrophysics Data System (ADS)

Cazade, Pierre-André; Tran, Halina; Bereau, Tristan; Das, Akshaya K.; Kläsi, Felix; Hamm, Peter; Meuwly, Markus

2015-06-01

The solvent dynamics around fluorinated acetonitrile is characterized by 2-dimensional infrared spectroscopy and atomistic simulations. The lineshape of the linear infrared spectrum is better captured by semiempirical (density functional tight binding) mixed quantum mechanical/molecular mechanics simulations, whereas force field simulations with multipolar interactions yield lineshapes that are significantly too narrow. For the solvent dynamics, a relatively slow time scale of 2 ps is found from the experiments and supported by the mixed quantum mechanical/molecular mechanics simulations. With multipolar force fields fitted to the available thermodynamical data, the time scale is considerably faster—on the 0.5 ps time scale. The simulations provide evidence for a well established CF-HOH hydrogen bond (population of 25%) which is found from the radial distribution function g(r) from both, force field and quantum mechanics/molecular mechanics simulations.
From molecular design and materials construction to organic nanophotonic devices.

PubMed

Zhang, Chuang; Yan, Yongli; Zhao, Yong Sheng; Yao, Jiannian

2014-12-16

CONSPECTUS: Nanophotonics has recently received broad research interest, since it may provide an alternative opportunity to overcome the fundamental limitations in electronic circuits. Diverse optical materials down to the wavelength scale are required to develop nanophotonic devices, including functional components for light emission, transmission, and detection. During the past decade, the chemists have made their own contributions to this interdisciplinary field, especially from the controlled fabrication of nanophotonic molecules and materials. In this context, organic micro- or nanocrystals have been developed as a very promising kind of building block in the construction of novel units for integrated nanophotonics, mainly due to the great versatility in organic molecular structures and their flexibility for the subsequent processing. Following the pioneering works on organic nanolasers and optical waveguides, the organic nanophotonic materials and devices have attracted increasing interest and developed rapidly during the past few years. In this Account, we review our research on the photonic performance of molecular micro- or nanostructures and the latest breakthroughs toward organic nanophotonic devices. Overall, the versatile features of organic materials are highlighted, because they brings tunable optical properties based on molecular design, size-dependent light confinement in low-dimensional structures, and various device geometries for nanophotonic integration. The molecular diversity enables abundant optical transitions in conjugated π-electron systems, and thus brings specific photonic functions into molecular aggregates. The morphology of these micro- or nanostructures can be further controlled based on the weak intermolecular interactions during molecular assembly process, making the aggregates show photon confinement or light guiding properties as nanophotonic materials. By adoption of some active processes in the composite of two or more materials, such as energy transfer, charge separation, and exciton-plasmon coupling, a series of novel nanophotonic devices could be achieved for light signal manipulation. First, we provide an overview of the research evolution of organic nanophotonics, which arises from attempts to explore the photonic potentials of low-dimensional structures assembled from organic molecules. Then, recent advances in this field are described from the viewpoints of molecules, materials, and devices. Many kinds of optofunctional molecules are designed and synthesized according to the demands in high luminescence yield, nonlinear optical response, and other optical properties. Due to the weak interactions between these molecules, numerous micro- or nanostructures could be prepared via self-assembly or vapor-deposition, bringing the capabilities of light transport and confinement at the wavelength scale. The above advantages provide great possibilities in the fabrication of organic nanophotonic devices, by rationally combining these functional components to manipulate light signals. Finally, we present our views on the current challenges as well as the future development of organic nanophotonic materials and devices. This Account gives a comprehensive understanding of organic nanophotonics, including the design and fabrication of organic micro- or nanocrystals with specific photonic properties and their promising applications in functional nanophotonic components and integrated circuits.
Molecular Gas Contents and Scaling Relations for Massive, Passive Galaxies at Intermediate Redshifts from the LEGA-C Survey

NASA Astrophysics Data System (ADS)

Spilker, Justin; Bezanson, Rachel; Barišić, Ivana; Bell, Eric; Lagos, Claudia del P.; Maseda, Michael; Muzzin, Adam; Pacifici, Camilla; Sobral, David; Straatman, Caroline; van der Wel, Arjen; van Dokkum, Pieter; Weiner, Benjamin; Whitaker, Katherine; Williams, Christina C.; Wu, Po-Feng

2018-06-01

A decade of study has established that the molecular gas properties of star-forming galaxies follow coherent scaling relations out to z ∼ 3, suggesting remarkable regularity of the interplay between molecular gas, star formation, and stellar growth. Passive galaxies, however, are expected to be gas-poor and therefore faint, and thus little is known about molecular gas in passive galaxies beyond the local universe. Here we present deep Atacama Large Millimeter/submillimeter Array observations of CO(2–1) emission in eight massive (M star ∼ 1011 M ⊙) galaxies at z ∼ 0.7 selected to lie a factor of 3–10 below the star-forming sequence at this redshift, drawn from the Large Early Galaxy Astrophysics Census survey. We significantly detect half the sample, finding molecular gas fractions ≲0.1. We show that the molecular and stellar rotational axes are broadly consistent, arguing that the molecular gas was not accreted after the galaxies became quiescent. We find that scaling relations extrapolated from the star-forming population overpredict both the gas fraction and gas depletion time for passive objects, suggesting the existence of either a break or large increase in scatter in these relations at low specific star formation rate. Finally, we show that the gas fractions of the passive galaxies we have observed at intermediate redshifts are naturally consistent with evolution into local, massive early-type galaxies by continued low-level star formation, with no need for further gas accretion or dynamical stabilization of the gas reservoirs in the intervening 6 billion years.
Regionally heterogeneous paleoenvironmental responses in the West African and South American monsoon systems on glacial to millennial timescales

NASA Astrophysics Data System (ADS)

Shanahan, T. M.; Hughen, K. A.; van Mooy, B.; Overpeck, J. T.; Baker, P. A.; Fritz, S.; Peck, J. A.; Scholz, C. A.; King, J. W.

2008-12-01

Although millennial-scale paleoenvironmental changes have been well characterized for high latitude sites, short-term climate variability in the tropics is less well understood. While the Intertropical Convergence Zone may act as an integrator of tropical climate changes, regional factors also play an important role in controlling the tropical response to climate forcing. Understanding these influences, and how they modulate the response to global climate forcing under different mean climate states is thus important for assessing how the tropics may respond to future climate change. Here, we examine new centennial-resolution records of paleoenvironmental change from isotopic and relative abundance data from molecular biomarkers in sediment cores from Lake Bosumtwi and Lake Titicaca. We assess the relative response of the West African and South American monsoon systems to millennial and suborbital-scale climate variability over the last ca. 30,000 years. While there is evidence for synchronous climate variability in the two systems, the dominant paleoenvironmental changes appear largely decoupled, highlighting the importance of regional climatology in controlling the response to climate forcing in tropical regions.
Free volume in ionic liquids: a connection of experimentally accessible observables from PALS and PVT experiments with the molecular structure from XRD data.

PubMed

Beichel, Witali; Yu, Yang; Dlubek, Günter; Krause-Rehberg, Reinhard; Pionteck, Jürgen; Pfefferkorn, Dirk; Bulut, Safak; Bejan, Dana; Friedrich, Christian; Krossing, Ingo

2013-06-14

In the current work, free volume concepts, primarily applied to glass formers in the literature, were transferred to ionic liquids (ILs). A series of 1-butyl-3-methylimidazolium ([C4MIM](+)) based ILs was investigated by Positron Annihilation Lifetime Spectroscopy (PALS). The phase transition and dynamic properties of the ILs [C4MIM][X] with [X](-) = [Cl](-), [BF4](-), [PF6](-), [OTf](-), [NTf2](-) and [B(hfip)4](-) were reported recently (Yu et al., Phys. Chem. Chem. Phys., 2012, 14, 6856-6868). In this subsequent work, attention was paid to the connection of the free volume from PALS (here the mean hole volume, ) with the molecular structure, represented by volumes derived from X-ray diffraction (XRD) data. These were the scaled molecular volume Vm,scaled and the van der Waals volume V(vdw). Linear correlations of at the "knee" temperature ((T(k))) with V(m,scaled) and V(vdw) gave good results for the [C4MIM](+) series. Further relationships between volumes from XRD data with the occupied volume Vocc determined from PALS/PVT (Pressure Volume Temperature) measurements and from Sanchez-Lacombe Equation of State (SL-EOS) fits were elaborated (V(occ)(SL-EOS) ≈ 1.63 V(vdw), R(2) = 0.981 and V(occ)(SL-EOS) ≈ 1.12 V(m,scaled), R(2) = 0.980). Finally, the usability of V(m,scaled) was justified in terms of the Cohen-Turnbull (CT) free volume theory. Empirical CT type plots of viscosity and electrical conductivity showed a systematic increase in the critical free volume with molecular size. Such correlations allow descriptions of IL properties with the easily accessible quantity V(m,scaled) within the context of the free volume.
Evaluation of Kirkwood-Buff integrals via finite size scaling: a large scale molecular dynamics study

NASA Astrophysics Data System (ADS)

Dednam, W.; Botha, A. E.

2015-01-01

Solvation of bio-molecules in water is severely affected by the presence of co-solvent within the hydration shell of the solute structure. Furthermore, since solute molecules can range from small molecules, such as methane, to very large protein structures, it is imperative to understand the detailed structure-function relationship on the microscopic level. For example, it is useful know the conformational transitions that occur in protein structures. Although such an understanding can be obtained through large-scale molecular dynamic simulations, it is often the case that such simulations would require excessively large simulation times. In this context, Kirkwood-Buff theory, which connects the microscopic pair-wise molecular distributions to global thermodynamic properties, together with the recently developed technique, called finite size scaling, may provide a better method to reduce system sizes, and hence also the computational times. In this paper, we present molecular dynamics trial simulations of biologically relevant low-concentration solvents, solvated by aqueous co-solvent solutions. In particular we compare two different methods of calculating the relevant Kirkwood-Buff integrals. The first (traditional) method computes running integrals over the radial distribution functions, which must be obtained from large system-size NVT or NpT simulations. The second, newer method, employs finite size scaling to obtain the Kirkwood-Buff integrals directly by counting the particle number fluctuations in small, open sub-volumes embedded within a larger reservoir that can be well approximated by a much smaller simulation cell. In agreement with previous studies, which made a similar comparison for aqueous co-solvent solutions, without the additional solvent, we conclude that the finite size scaling method is also applicable to the present case, since it can produce computationally more efficient results which are equivalent to the more costly radial distribution function method.

A SCALE-UP Mock-Up: Comparison of Student Learning Gains in High- and Low-Tech Active-Learning Environments

PubMed Central

Soneral, Paula A. G.; Wyse, Sara A.

2017-01-01

Student-centered learning environments with upside-down pedagogies (SCALE-UP) are widely implemented at institutions across the country, and learning gains from these classrooms have been well documented. This study investigates the specific design feature(s) of the SCALE-UP classroom most conducive to teaching and learning. Using pilot survey data from instructors and students to prioritize the most salient SCALE-UP classroom features, we created a low-tech “Mock-up” version of this classroom and tested the impact of these features on student learning, attitudes, and satisfaction using a quasi-experimental setup. The same instructor taught two sections of an introductory biology course in the SCALE-UP and Mock-up rooms. Although students in both sections were equivalent in terms of gender, grade point average, incoming ACT, and drop/fail/withdraw rate, the Mock-up classroom enrolled significantly more freshmen. Controlling for class standing, multiple regression modeling revealed no significant differences in exam, in-class, preclass, and Introduction to Molecular and Cellular Biology Concept Inventory scores between the SCALE-UP and Mock-up classrooms. Thematic analysis of student comments highlighted that collaboration and whiteboards enhanced the learning experience, but technology was not important. Student satisfaction and attitudes were comparable. These results suggest that the benefits of a SCALE-UP experience can be achieved at lower cost without technology features. PMID:28213582
Patterned self-assembled monolayers for nanoscale lithography and the control of catalytically produced electroosmosis

NASA Astrophysics Data System (ADS)

Subramanian, Shyamala

This thesis explores two applications of self-assembled monolayers (SAMs) (a) for developing novel molecular assembly based nanolithography techniques and (b) for tailoring zeta-potential of surfaces towards achieving directional control of catalytically induced fluid flow. The first half of the thesis develops the process of molecular ruler lithography using sacrificial host structures. This is a novel hybrid nanolithography technique which combines chemical self-assembly with conventional fabrication methods for improving the resolution of existing lithography tools to sub-50 nm. Previous work related to molecular ruler lithography have shown the use of thiol-SAMs, placed one on top of the other like a molecular resist, for scaling down feature sizes. In this thesis various engineering solutions for improving the reproducibility, yield, nanoscale roughness and overall manufacturability of the process are introduced. This is achieved by introducing a sacrificial inert layer underneath the gold parent structure. This bilayer sacrificial host allows for preferential, easy and quick removal of the parent structures, isolates the parent metal from the underlying substrate and improves reproducibility of the lift-off process. Also it opens avenues for fabrication of high aspect ratio features. Also molecular layer vapor deposition method is developed for building the multilayer molecular resist via vapor phase to reduce contaminations and yield issues associated with solution phase deposition. The smallest isolated metal features produced using this process were 40 nm in width. The second half of the thesis describes application of thiol-SAMs to tailor surface properties of gold, specifically the surface charge or zeta potential. Previous work has demonstrated that the direction of movement of fluid in the vicinity of a catalytically active bimetallic junction placed in a solution of dilute hydrogen peroxide depends on the charge of the gold surface. SAMs with different end-group functionality impart different surface zeta potential to the gold surface. Zeta-potential engineering via patterning various end-group functionalized SAMs on gold surface to control direction of catalytically induced electroosmotic fluid flow is demonstrated for the first time. This work also describes the application of catalytic power to produce controlled rotational motion. Gold gears-like structures made using conventional microfabrication techniques and propelled by catalytic power are shown to rotate at speeds of 1 rotation/sec in a dilute solution of hydrogen peroxide. Fabrication of a force sensor for detection and measurement of catalytic forces is also introduced. The force sensor, with sensitivity in the piconewton range, consists of a microcantilever with a catalytically active silver post patterned on the tip. Changes in cantilever displacement and resonance frequency due to the catalytic force were monitored as a function of concentration of hydrogen peroxide. Overall, this thesis integrates SAM deposition and patterning techniques with conventional fabrication methods to engineer and control nanoscale structures and devices. Possible future device designs are described including CMOS devices having channel width defined using molecular ruler lithography with sacrificial hosts, drug delivery device based on AFM force sensor and channeless pumps powered by catalytic reactions with SAM controlled electroosmotic fluid flow.
Environmental controls on leaf wax δD ratios in surface peats across the monsoonal region of China

NASA Astrophysics Data System (ADS)

Huang, X.; Xue, J.; Wang, X.; Meyers, P. A.

2015-09-01

Leaf wax molecular and isotopic ratios are generally considered robust isotopic paleohydrologic proxies. Here we evaluate the proxy value of the molecular distributions and hydrogen isotopic compositions of long chain n-alkanes (δDalk) in surface peats collected from peatlands across a range of annual air temperatures from 1 to 15 °C and a range of annual mean precipitation from 720 to 2070 mm in the monsoonal region of China. The alkane ratios (ACL and CPI) and δDalk values show relatively large variations in multiple samples from a single site, highlighting the complexity of these ratios at a small spatial scale. In the montane Zoigê peatland, the apparent fractionation between precipitation and δDalk is more positive than in the other six sites, which is possibly an effect of the higher conductivity of the water in this high elevation site (3500 m a.s.l.). At a larger spatial scale, the site-averaged CPI ratios and the δDalk values of n-C29 and n-C31 alkanes show significant correlation with the air temperature and precipitation. These results support the application of the CPI ratio and the δDalk ratios of n-C29 and n-C31 alkanes as sensitive paleohydrologic proxies on millennial and larger timescales.
3D Printing of Molecular Models

ERIC Educational Resources Information Center

Gardner, Adam; Olson, Arthur

2016-01-01

Physical molecular models have played a valuable role in our understanding of the invisible nano-scale world. We discuss 3D printing and its use in producing models of the molecules of life. Complex biomolecular models, produced from 3D printed parts, can demonstrate characteristics of molecular structure and function, such as viral self-assembly,…
Line overlap and self-shielding of molecular hydrogen in galaxies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gnedin, Nickolay Y.; Draine, Bruce T., E-mail: gnedin@fnal.gov, E-mail: andrey@oddjob.uchicago.edu, E-mail: draine@astro.princeton.edu

2014-11-01

The effect of line overlap in the Lyman and Werner bands, often ignored in galactic studies of the atomic-to-molecular transition, greatly enhances molecular hydrogen self-shielding in low metallicity environments and dominates over dust shielding for metallicities below about 10% solar. We implement that effect in cosmological hydrodynamics simulations with an empirical model, calibrated against the observational data, and provide fitting formulae for the molecular hydrogen fraction as a function of gas density on various spatial scales and in environments with varied dust abundance and interstellar radiation field. We find that line overlap, while important for detailed radiative transfer in themore » Lyman and Werner bands, has only a minor effect on star formation on galactic scales, which, to a much larger degree, is regulated by stellar feedback.« less
What can molecular dynamics simulations reveal about the stability of proteinaceous soil organic matter on mineral surfaces?

NASA Astrophysics Data System (ADS)

Andersen, A.; Reardon, P. N.; Chacon, S. S.; Qafoku, N. P.; Washton, N.; Kleber, M.

2015-12-01

With the increased attention on climate change and the role of increasing atmospheric CO2 levels in global warming, the need for an accurate depiction of the carbon cycling processes involved in the Earth's three major carbon pools, i.e., atmosphere, terrestrial systems, and oceans has never been greater. Within the terrestrial system, soil organic matter (SOM) represents an important carbon sub-pool. Complexation of SOM with mineral interfaces and particles is believed to protect SOM from possible biotic and abiotic transformation and mineralization to carbon dioxide. However, obtaining a molecular scale picture of the interactions of the various types of SOM with a variety of soil minerals is a challenging endeavor, especially for experimental techniques. Molecular scale simulations techniques can be applied to study the atomistic, molecular, and nanoscale aspects of SOM-mineral associations, and, therefore, and aid in filling current knowledge gaps in the potential fate and stability of SOM in soil systems. Here, we will discuss our recent results from large-scale molecular dynamics simulation of protein, GB1, and its interaction with clay and oxide/hydroxide minerals (i.e., kaolinite, Na+-MMT, Ca2+-MMT, goethite, and birnessite) including a comparison of structural changes of the protein by, protein orientation with respect to, degree of protein binding to, and mobility on the mineral surfaces. Our molecular simulations indicate that these mineral surfaces, with the exception of birnessite, potentially preserve the physical properties of the GB1 protein.
Controlling carbon-nanotube-phospholipid solubility by curvature-dependent self-assembly.

PubMed

Määttä, Jukka; Vierros, Sampsa; Sammalkorpi, Maria

2015-03-12

Control of aqueous dispersion is central in the processing and usage of nanoscale hydrophobic objects. However, selecting dispersive agents based on the size and form of the hydrophobic object and the role of coating morphology in dispersion efficiency remain important open questions. Here, the effect of the substrate and the dispersing molecule curvature, as well as, the influence of dispersant concentration on the adsorption morphology are examined by molecular simulations of graphene and carbon nanotube (CNT) substrates with phospholipids of varying curvature as the dispersing agents. Lipid spontaneous curvature is increased from close to zero (effectively cylindrical lipid) to highly positive (effectively conical lipid) by studying double tailed dipalmitoylphosphadidylcholine (DPPC) and single tailed lysophosphadidylcholine (LPC) which differ in the number of acyl chains but have identical headgroup. We find that lipids are good dispersion agents for both planar and curved nanoparticles and induce a dispersive barrier nonsize selectively. Differences in dispersion efficiency arise from lipid headgroup density and their extension from the hydrophobic substrate in the adsorption morphology. We map the packing morphology contributing factors and report that the aggregate morphologies depend on the competition of interactions rising from (1) hydrophobicity driven maximization of lipid-substrate contacts and lipid self-adhesion, (2) tail bending energy cost, (3) preferential alignment along the graphitic substrate principal axes, and (4) lipid headgroup preferential packing. Curved substrates adjust the morphology by changing the balance between the interaction strengths. Jointly, the findings show substrate curvature and dimensions are a way to tune lipid adsorption to desired, self-assembling patterns. Besides engineering dispersion efficiency, the findings could bear significance in designing materials with defined molecular scale, molecular coatings for orientation specific CNT assembly or lipid-based molecular masks and patterning on graphene.
Optically Defined Multifunctional Patterning of Photosensitive Thin-Film Silica Mesophases

NASA Astrophysics Data System (ADS)

Doshi, Dhaval A.; Huesing, Nicola K.; Lu, Mengcheng; Fan, Hongyou; Lu, Yunfeng; Simmons-Potter, Kelly; Potter, B. G.; Hurd, Alan J.; Brinker, C. Jeffrey

2000-10-01

Photosensitive films incorporating molecular photoacid generators compartmentalized within a silica-surfactant mesophase were prepared by an evaporation-induced self-assembly process. Ultraviolet exposure promoted localized acid-catalyzed siloxane condensation, which can be used for selective etching of unexposed regions; for ``gray-scale'' patterning of refractive index, pore size, surface area, and wetting behavior; and for optically defining a mesophase transformation (from hexagonal to tetragonal) within the film. The ability to optically define and continuously control both structure and function on the macro- and mesoscales is of interest for sensor arrays, nanoreactors, photonic and fluidic devices, and low-dielectric-constant films.
2.3. Global-scale atmospheric dispersion of microorganisms

USGS Publications Warehouse

Griffin, Dale W.; Gonzalez-Martin, Cristina; Hoose, C.; Smith, D.J.; Delort, Anne-Marie; Amato, Pierre

2018-01-01

This chapter addresses long-range dispersion and the survival of microorganisms across a wide range of altitudes in Earth's atmosphere. Topics include mechanisms of dispersion, survivability of microorganisms known to be associated with long-range transport, natural and artificial sources of bioaerosols, residence time estimation through the use of proxy aerosols, transport and emission models, and monitoring assays (both culture and molecular based). We conclude with a discussion of the known limits for Earth's biosphere boundary, relating aerobiology studies to planetary exploration given the large degree of overlapping requirements for in situ studies (including low biomass life detection and contamination control).
DOE Office of Scientific and Technical Information (OSTI.GOV)

Rizzi, Silvio; Hereld, Mark; Insley, Joseph

In this work we perform in-situ visualization of molecular dynamics simulations, which can help scientists to visualize simulation output on-the-fly, without incurring storage overheads. We present a case study to couple LAMMPS, the large-scale molecular dynamics simulation code with vl3, our parallel framework for large-scale visualization and analysis. Our motivation is to identify effective approaches for covisualization and exploration of large-scale atomistic simulations at interactive frame rates.We propose a system of coupled libraries and describe its architecture, with an implementation that runs on GPU-based clusters. We present the results of strong and weak scalability experiments, as well as future researchmore » avenues based on our results.« less
Observation time scale, free-energy landscapes, and molecular symmetry

PubMed Central

Wales, David J.; Salamon, Peter

2014-01-01

When structures that interconvert on a given time scale are lumped together, the corresponding free-energy surface becomes a function of the observation time. This view is equivalent to grouping structures that are connected by free-energy barriers below a certain threshold. We illustrate this time dependence for some benchmark systems, namely atomic clusters and alanine dipeptide, highlighting the connections to broken ergodicity, local equilibrium, and “feasible” symmetry operations of the molecular Hamiltonian. PMID:24374625
Energetic basis for the molecular-scale organization of bone

DOE PAGES

Tao, Jinhui; Battle, Keith C.; Pan, Haihua; ...

2014-12-24

Here, the remarkable properties of bone derive from a highly organized arrangement of co-aligned nm-scale apatite platelets within a fibrillar collagen matrix. The origin of this arrangement is poorly understood and the crystal structures of hydroxyapatite (HAP) and the non-mineralized collagen fibrils alone do not provide an explanation. Moreover, little is known about collagen-apatite interaction energies, which should strongly influence both the molecular-scale organization and the resulting mechanical properties of the composite. We investigated collagen-mineral interactions by combining dynamic force spectroscopy (DFS) measurements of binding energies with molecular dynamics (MD) simulations of binding and AFM observations of collagen adsorption onmore » single crystals of calcium phosphate for four mineral phases of potential importance in bone formation. In all cases, we observe a strong preferential orientation of collagen binding, but comparison between the observed orientations and TEM analyses native tissues shows only calcium-deficient apatite (CDAP) provides an interface with collagen that is consistent with both. MD simulations predict preferred collagen orientations that agree with observations and results from both MD and DFS reveal large values for the binding energy due to multiple binding sites. These findings reconcile apparent contradictions inherent in a hydroxyapatite or carbonated apatite (CAP) model of bone mineral and provide an energetic rationale for the molecular scale organization of bone.« less
Unraveling Hydrophobic Interactions at the Molecular Scale Using Force Spectroscopy and Molecular Dynamics Simulations.

PubMed

Stock, Philipp; Monroe, Jacob I; Utzig, Thomas; Smith, David J; Shell, M Scott; Valtiner, Markus

2017-03-28

Interactions between hydrophobic moieties steer ubiquitous processes in aqueous media, including the self-organization of biologic matter. Recent decades have seen tremendous progress in understanding these for macroscopic hydrophobic interfaces. Yet, it is still a challenge to experimentally measure hydrophobic interactions (HIs) at the single-molecule scale and thus to compare with theory. Here, we present a combined experimental-simulation approach to directly measure and quantify the sequence dependence and additivity of HIs in peptide systems at the single-molecule scale. We combine dynamic single-molecule force spectroscopy on model peptides with fully atomistic, both equilibrium and nonequilibrium, molecular dynamics (MD) simulations of the same systems. Specifically, we mutate a flexible (GS) 5 peptide scaffold with increasing numbers of hydrophobic leucine monomers and measure the peptides' desorption from hydrophobic self-assembled monolayer surfaces. Based on the analysis of nonequilibrium work-trajectories, we measure an interaction free energy that scales linearly with 3.0-3.4 k B T per leucine. In good agreement, simulations indicate a similar trend with 2.1 k B T per leucine, while also providing a detailed molecular view into HIs. This approach potentially provides a roadmap for directly extracting qualitative and quantitative single-molecule interactions at solid/liquid interfaces in a wide range of fields, including interactions at biointerfaces and adhesive interactions in industrial applications.
Shock Wave Propagation in Cementitious Materials at Micro/Meso Scales

NASA Astrophysics Data System (ADS)

Rajendran, Arunachalam

2015-06-01

The mechanical and constitutive response of materials like cement, and bio materials like fish scale and abalone shell is very complex due to heterogeneities that are inherently present in the nano and microstructures. The intrinsic constitutive behaviors are driven by the chemical composition and the molecular, micro, and meso structures. Therefore, it becomes important to identify the material genome as the building block for the material. For instance, in cementitious materials, the genome of C-S-H phase (the glue or the paste) that holds the various clinkers, such as the dicalcium silicate, tricalcium silicate, calcium ferroaluminates, and others is extremely complex. Often mechanical behaviors of C-S-H type materials are influenced by the chemistry and the structures at all nano to micro length scales. By explicitly modeling the molecular structures using appropriate potentials, it is then possible to compute the elastic tensor from molecular dynamics simulations using all atom method. The elastic tensors for the C-S-H gel and other clinkers are determined using the software suite ``Accelrys Materials Studio.'' A strain rate dependent, fracture mechanics based tensile damage model has been incorporated into ABAQUS finite element code to model spall evolution in the heterogeneous cementitious material with all constituents explicitly modeled through one micron element resolution. This paper presents results from nano/micro/meso scale analyses of shock wave propagation in a heterogeneous cementitious material using both molecular dynamic and finite element codes.
Energetic basis for the molecular-scale organization of bone.

PubMed

Tao, Jinhui; Battle, Keith C; Pan, Haihua; Salter, E Alan; Chien, Yung-Ching; Wierzbicki, Andrzej; De Yoreo, James J

2015-01-13

The remarkable properties of bone derive from a highly organized arrangement of coaligned nanometer-scale apatite platelets within a fibrillar collagen matrix. The origin of this arrangement is poorly understood and the crystal structures of hydroxyapatite (HAP) and the nonmineralized collagen fibrils alone do not provide an explanation. Moreover, little is known about collagen-apatite interaction energies, which should strongly influence both the molecular-scale organization and the resulting mechanical properties of the composite. We investigated collagen-mineral interactions by combining dynamic force spectroscopy (DFS) measurements of binding energies with molecular dynamics (MD) simulations of binding and atomic force microscopy (AFM) observations of collagen adsorption on single crystals of calcium phosphate for four mineral phases of potential importance in bone formation. In all cases, we observe a strong preferential orientation of collagen binding, but comparison between the observed orientations and transmission electron microscopy (TEM) analyses of native tissues shows that only calcium-deficient apatite (CDAP) provides an interface with collagen that is consistent with both. MD simulations predict preferred collagen orientations that agree with observations, and results from both MD and DFS reveal large values for the binding energy due to multiple binding sites. These findings reconcile apparent contradictions inherent in a hydroxyapatite or carbonated apatite (CAP) model of bone mineral and provide an energetic rationale for the molecular-scale organization of bone.
Exploring molecular variation in Schistosoma japonicum in China.

PubMed

Young, Neil D; Chan, Kok-Gan; Korhonen, Pasi K; Min Chong, Teik; Ee, Robson; Mohandas, Namitha; Koehler, Anson V; Lim, Yan-Lue; Hofmann, Andreas; Jex, Aaron R; Qian, Baozhen; Chilton, Neil B; Gobert, Geoffrey N; McManus, Donald P; Tan, Patrick; Webster, Bonnie L; Rollinson, David; Gasser, Robin B

2015-12-01

Schistosomiasis is a neglected tropical disease that affects more than 200 million people worldwide. The main disease-causing agents, Schistosoma japonicum, S. mansoni and S. haematobium, are blood flukes that have complex life cycles involving a snail intermediate host. In Asia, S. japonicum causes hepatointestinal disease (schistosomiasis japonica) and is challenging to control due to a broad distribution of its snail hosts and range of animal reservoir hosts. In China, extensive efforts have been underway to control this parasite, but genetic variability in S. japonicum populations could represent an obstacle to eliminating schistosomiasis japonica. Although a draft genome sequence is available for S. japonicum, there has been no previous study of molecular variation in this parasite on a genome-wide scale. In this study, we conducted the first deep genomic exploration of seven S. japonicum populations from mainland China, constructed phylogenies using mitochondrial and nuclear genomic data sets, and established considerable variation between some of the populations in genes inferred to be linked to key cellular processes and/or pathogen-host interactions. Based on the findings from this study, we propose that verifying intraspecific conservation in vaccine or drug target candidates is an important first step toward developing effective vaccines and chemotherapies against schistosomiasis.
Development of cost-effective noncarbon sorbents for Hg(0) removal from coal-fired power plants.

PubMed

Lee, Joo-Youp; Ju, Yuhong; Keener, Tim C; Varma, Rajender S

2006-04-15

Noncarbonaceous materials or mineral oxides (silica gel, alumina, molecular sieves, zeolites, and montmorillonite) were modified with various functional groups such as amine, amide, thiol, urea, and active additives such as elemental sulfur, sodium sulfide, and sodium polysulfide to examine their potential as sorbents for the removal of elemental mercury (Hg(0)) vapor at coal-fired utility power plants. A number of sorbent candidates such as amine- silica gel, urea- silica gel, thiol- silica gel, amide-silica gel, sulfur-alumina, sulfur-molecular sieve, sulfur-montmorillonite, sodium sulfide-montmorillonite, and sodium polysulfide-montmorillonite, were synthesized and tested in a lab-scale fixed-bed system under an argon flow for screening purposes at 70 degrees C and/or 140 degrees C. Several functionalized silica materials reported in previous studies to effectively control heavy metals in the aqueous phase showed insignificant adsorption capacities for Hg(0) control in the gas phase, suggesting that mercury removal mechanisms in both phases are different. Among elemental sulfur-, sodium sulfide-, and sodium polysulfide-impregnated inorganic samples, sodium polysulfide-impregnated montmorillonite K 10 showed a moderate adsorption capacity at 70 degrees C, which can be used for sorbent injection prior to the wet FGD system.
Assessment of novel maleic anhydride copolymers prepared via nitroxide-mediated radical polymerization as CaSO4 crystal growth inhibitors.

PubMed

Al-Roomi, Yousef Mohammad; Hussain, Kaneez Fatema

2017-04-01

Calcium sulfate is one of the dominant scales which, unlike carbonate scale, are not easily removable by acid. To inhibit CaSO 4 scale formation in artificial cooling water systems, well-defined low molecular weight maleic anhydride and n-alkylacrylamide copolymers (YMR-S series) were synthesized via nitroxide-mediated radical polymerization initiated by benzoyl peroxide in the presence of 2,2,6,6-tetramethyl-1-piperidinyloxy at varying concentrations. These polymerizations exhibit living polymerization characteristics; that is, they show linear growth in chain length as a function of monomer conversion, and have narrow molecular weight distributions. Resultant polymers were characterized by means of 1 H-NMR and 13 C-NMR. The inhibition behavior of these YMR-S series polymers against CaSO 4 was evaluated using the static scale inhibition method and a dynamic tube block test. The inhibition ability on the CaSO 4 scale is 99.5% with 9 ppm dosage level at pH 10.45 and temperature 70°C. Scanning electronic microscope analysis proved the morphological changes of the CaSO 4 scales due to the strong inhibition action of YMR-S polymers. It is also observed that the antiscaling effect of the copolymers greatly depends on the molecular weight, and the optimum range is below 20,000 and approximately in the range 500-2000.
PHIBSS: Unified Scaling Relations of Gas Depletion Time and Molecular Gas Fractions

NASA Astrophysics Data System (ADS)

Tacconi, L. J.; Genzel, R.; Saintonge, A.; Combes, F.; García-Burillo, S.; Neri, R.; Bolatto, A.; Contini, T.; Förster Schreiber, N. M.; Lilly, S.; Lutz, D.; Wuyts, S.; Accurso, G.; Boissier, J.; Boone, F.; Bouché, N.; Bournaud, F.; Burkert, A.; Carollo, M.; Cooper, M.; Cox, P.; Feruglio, C.; Freundlich, J.; Herrera-Camus, R.; Juneau, S.; Lippa, M.; Naab, T.; Renzini, A.; Salome, P.; Sternberg, A.; Tadaki, K.; Übler, H.; Walter, F.; Weiner, B.; Weiss, A.

2018-02-01

This paper provides an update of our previous scaling relations between galaxy-integrated molecular gas masses, stellar masses, and star formation rates (SFRs), in the framework of the star formation main sequence (MS), with the main goal of testing for possible systematic effects. For this purpose our new study combines three independent methods of determining molecular gas masses from CO line fluxes, far-infrared dust spectral energy distributions, and ∼1 mm dust photometry, in a large sample of 1444 star-forming galaxies between z = 0 and 4. The sample covers the stellar mass range log(M */M ⊙) = 9.0–11.8, and SFRs relative to that on the MS, δMS = SFR/SFR(MS), from 10‑1.3 to 102.2. Our most important finding is that all data sets, despite the different techniques and analysis methods used, follow the same scaling trends, once method-to-method zero-point offsets are minimized and uncertainties are properly taken into account. The molecular gas depletion time t depl, defined as the ratio of molecular gas mass to SFR, scales as (1 + z)‑0.6 × (δMS)‑0.44 and is only weakly dependent on stellar mass. The ratio of molecular to stellar mass μ gas depends on (1+z{)}2.5× {(δ {MS})}0.52× {({M}* )}-0.36, which tracks the evolution of the specific SFR. The redshift dependence of μ gas requires a curvature term, as may the mass dependences of t depl and μ gas. We find no or only weak correlations of t depl and μ gas with optical size R or surface density once one removes the above scalings, but we caution that optical sizes may not be appropriate for the high gas and dust columns at high z. Based on observations of an IRAM Legacy Program carried out with the NOEMA, operated by the Institute for Radio Astronomy in the Millimetre Range (IRAM), which is funded by a partnership of INSU/CNRS (France), MPG (Germany), and IGN (Spain).
Unconventional Current Scaling and Edge Effects for Charge Transport through Molecular Clusters

PubMed Central

2017-01-01

Metal–molecule–metal junctions are the key components of molecular electronics circuits. Gaining a microscopic understanding of their conducting properties is central to advancing the field. In the present contribution, we highlight the fundamental differences between single-molecule and ensemble junctions focusing on the fundamentals of transport through molecular clusters. In this way, we elucidate the collective behavior of parallel molecular wires, bridging the gap between single molecule and large-area monolayer electronics, where even in the latter case transport is usually dominated by finite-size islands. On the basis of first-principles charge-transport simulations, we explain why the scaling of the conductivity of a junction has to be distinctly nonlinear in the number of molecules it contains. Moreover, transport through molecular clusters is found to be highly inhomogeneous with pronounced edge effects determined by molecules in locally different electrostatic environments. These effects are most pronounced for comparably small clusters, but electrostatic considerations show that they prevail also for more extended systems. PMID:29043825

Vertical resonant tunneling transistors with molecular quantum dots for large-scale integration.

PubMed

Hayakawa, Ryoma; Chikyow, Toyohiro; Wakayama, Yutaka

2017-08-10

Quantum molecular devices have a potential for the construction of new data processing architectures that cannot be achieved using current complementary metal-oxide-semiconductor (CMOS) technology. The relevant basic quantum transport properties have been examined by specific methods such as scanning probe and break-junction techniques. However, these methodologies are not compatible with current CMOS applications, and the development of practical molecular devices remains a persistent challenge. Here, we demonstrate a new vertical resonant tunneling transistor for large-scale integration. The transistor channel is comprised of a MOS structure with C 60 molecules as quantum dots, and the structure behaves like a double tunnel junction. Notably, the transistors enabled the observation of stepwise drain currents, which originated from resonant tunneling via the discrete molecular orbitals. Applying side-gate voltages produced depletion layers in Si substrates, to achieve effective modulation of the drain currents and obvious peak shifts in the differential conductance curves. Our device configuration thus provides a promising means of integrating molecular functions into future CMOS applications.
The Molecular Registry of Pituitary Adenomas (REMAH): A bet of Spanish Endocrinology for the future of individualized medicine and translational research.

PubMed

Luque, Raúl M; Ibáñez-Costa, Alejandro; Sánchez-Tejada, Laura; Rivero-Cortés, Esther; Robledo, Mercedes; Madrazo-Atutxa, Ainara; Mora, Mireia; Álvarez, Clara V; Lucas-Morante, Tomás; Álvarez-Escolá, Cristina; Fajardo, Carmen; Castaño, Luis; Gaztambide, Sonia; Venegas-Moreno, Eva; Soto-Moreno, Alfonso; Gálvez, María Ángeles; Salvador, Javier; Valassi, Elena; Webb, Susan M; Picó, Antonio; Puig-Domingo, Manel; Gilabert, Montserrat; Bernabéu, Ignacio; Marazuela, Mónica; Leal-Cerro, Alfonso; Castaño, Justo P

2016-01-01

Pituitary adenomas are uncommon, difficult to diagnose tumors whose heterogeneity and low incidence complicate large-scale studies. The Molecular Registry of Pituitary Adenomas (REMAH) was promoted by the Andalusian Society of Endocrinology and Nutrition (SAEN) in 2008 as a cooperative clinical-basic multicenter strategy aimed at improving diagnosis and treatment of pituitary adenomas by combining clinical, pathological, and molecular information. In 2010, the Spanish Society of Endocrinology and Nutrition (SEEN) extended this project to national level and established 6 nodes with common protocols and methods for sample and clinical data collection, molecular analysis, and data recording in a common registry (www.remahnacional.com). The registry combines clinical data with molecular phenotyping of the resected pituitary adenoma using quantitative real-time PCR of expression of 26 genes: Pituitary hormones (GH-PRL-LH-FSH-PRL-ACTH-CGA), receptors (somatostatin, dopamine, GHRH, GnRH, CRH, arginine-vasopressin, ghrelin), other markers (Ki67, PTTG1), and control genes. Until 2015, molecular information has been collected from 704 adenomas, out of 1179 patients registered. This strategy allows for comparative and relational analysis between the molecular profile of the different types of adenoma and the clinical phenotype of patients, which may provide a better understanding of the condition and potentially help in treatment selection. The REMAH is therefore a unique multicenter, interdisciplinary network founded on a shared database that provides a far-reaching translational approach for management of pituitary adenomas, and paves the way for the conduct of combined clinical-basic innovative studies on large patient samples. Copyright © 2016 SEEN. Published by Elsevier España, S.L.U. All rights reserved.
DNA Nanotechnology for Precise Control over Drug Delivery and Gene Therapy.

PubMed

Angell, Chava; Xie, Sibai; Zhang, Liangfang; Chen, Yi

2016-03-02

Nanomedicine has been growing exponentially due to its enhanced drug targeting and reduced drug toxicity. It uses the interactions where nanotechnological components and biological systems communicate with each other to facilitate the delivery performance. At this scale, the physiochemical properties of delivery systems strongly affect their capacities. Among current delivery systems, DNA nanotechnology shows many advantages because of its unprecedented engineering abilities. Through molecular recognition, DNA nanotechnology can be used to construct a variety of nanostructures with precisely controllable size, shape, and surface chemistry, which can be appreciated in the delivery process. In this review, different approaches that are currently used for the construction of DNA nanostructures are reported. Further, the utilization of these DNA nanostructures with the well-defined parameters for the precise control in drug delivery and gene therapy is discussed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
A polyhedron made of tRNAs

PubMed Central

Severcan, Isil; Geary, Cody; Chworos, Arkadiusz; Voss, Neil; Jacovetty, Erica; Jaeger, Luc

2010-01-01

Supra-molecular assembly is a powerful strategy used by nature for building nano-scale architectures with predefined sizes and shapes. Numerous challenges remain however to be solved in order to demonstrate precise control over the synthesis, folding and assembly of rationally designed three-dimensional (3D) nano-objects made of RNA. Using the transfer RNA molecule as a structural building block, we report the design, efficient synthesis and structural characterization of stable, modular 3D particles adopting the polyhedral geometry of a non-uniform square antiprism. The spatial control within the final architecture allows precise positioning and encapsulation of proteins. This work demonstrates that a remarkable degree of structural control can be achieved with RNA structural motifs to build thermostable 3D nano-architectures that do not rely on helix bundles or tensegrity. RNA 3D particles can potentially be used as carriers or scaffolds in nano-medicine and synthetic biology. PMID:20729899
Localized diffusive motion on two different time scales in solid alkane nanoparticles

NASA Astrophysics Data System (ADS)

Wang, S.-K.; Mamontov, E.; Bai, M.; Hansen, F. Y.; Taub, H.; Copley, J. R. D.; García Sakai, V.; Gasparovic, G.; Jenkins, T.; Tyagi, M.; Herwig, K. W.; Neumann, D. A.; Montfrooij, W.; Volkmann, U. G.

2010-09-01

High-energy-resolution quasielastic neutron scattering on three complementary spectrometers has been used to investigate molecular diffusive motion in solid nano- to bulk-sized particles of the alkane n-C32H66. The crystalline-to-plastic and plastic-to-fluid phase transition temperatures are observed to decrease as the particle size decreases. In all samples, localized molecular diffusive motion in the plastic phase occurs on two different time scales: a "fast" motion corresponding to uniaxial rotation about the long molecular axis; and a "slow" motion attributed to conformational changes of the molecule. Contrary to the conventional interpretation in bulk alkanes, the fast uniaxial rotation begins in the low-temperature crystalline phase.
Coarse-graining to the meso and continuum scales with molecular-dynamics-like models

NASA Astrophysics Data System (ADS)

Plimpton, Steve

Many engineering-scale problems that industry or the national labs try to address with particle-based simulations occur at length and time scales well beyond the most optimistic hopes of traditional coarse-graining methods for molecular dynamics (MD), which typically start at the atomic scale and build upward. However classical MD can be viewed as an engine for simulating particles at literally any length or time scale, depending on the models used for individual particles and their interactions. To illustrate I'll highlight several coarse-grained (CG) materials models, some of which are likely familiar to molecular-scale modelers, but others probably not. These include models for water droplet freezing on surfaces, dissipative particle dynamics (DPD) models of explosives where particles have internal state, CG models of nano or colloidal particles in solution, models for aspherical particles, Peridynamics models for fracture, and models of granular materials at the scale of industrial processing. All of these can be implemented as MD-style models for either soft or hard materials; in fact they are all part of our LAMMPS MD package, added either by our group or contributed by collaborators. Unlike most all-atom MD simulations, CG simulations at these scales often involve highly non-uniform particle densities. So I'll also discuss a load-balancing method we've implemented for these kinds of models, which can improve parallel efficiencies. From the physics point-of-view, these models may be viewed as non-traditional or ad hoc. But because they are MD-style simulations, there's an opportunity for physicists to add statistical mechanics rigor to individual models. Or, in keeping with a theme of this session, to devise methods that more accurately bridge models from one scale to the next.
Seeing the Forest Through the Trees: The Distribution and Properties of Dense Molecular Gas in the Milky Way Galaxy

NASA Astrophysics Data System (ADS)

Ellsworth-Bowers, Timothy P.

The Milky Way Galaxy serves as a vast laboratory for studying the dynamics and evolution of the dense interstellar medium and the processes of and surrounding massive star formation. From our vantage point within the Galactic plane, however, it has been extremely difficult to construct a coherent picture of Galactic structure; we cannot see the forest for the trees. The principal difficulties in studying the structure of the Galactic disk have been obscuration by the ubiquitous dust and molecular gas and confusion between objects along a line of sight. Recent technological advances have led to large-scale blind surveys of the Galactic plane at (sub-)millimeter wavelengths, where Galactic dust is generally optically thin, and have opened a new avenue for studying the forest. The Bolocam Galactic Plane Survey (BGPS) observed over 190 deg 2 of the Galactic plane in dust continuum emission near lambda = 1.1 mm, producing a catalog of over 8,000 dense molecular cloud structures across a wide swath of the Galactic disk. Deriving the spatial distribution and physical properties of these objects requires knowledge of distance, a component lacking in the data themselves. This thesis presents a generalized Bayesian probabilistic distance estimation method for dense molecular cloud structures, and demonstrates it with the BGPS data set. Distance probability density functions (DPDFs) are computed from kinematic distance likelihoods (which may be double- peaked for objects in the inner Galaxy) and an expandable suite of prior information to produce a comprehensive tally of our knowledge (and ignorance) of the distances to dense molecular cloud structures. As part of the DPDF formalism, this thesis derives several prior DPDFs for resolving the kinematic distance ambiguity in the inner Galaxy. From the collection of posterior DPDFs, a set of objects with well-constrained distance estimates is produced for deriving Galactic structure and the physical properties of dense molecular cloud structures. This distance catalog of 1,802 objects across the Galactic plane represents the first large-scale analysis of clump-scale objects in a variety of Galactic environments. The Galactocentric positions of these objects begin to trace out the spiral structure of the Milky Way, and suggest that dense molecular gas settles nearer the Galactic midplane than tracers of less-dense gas such as CO. Physical properties computed from the DPDFs reveal that BGPS objects trace a continuum of scales within giant molecular clouds, and extend the scaling relationships known as Larson's Laws to lower-mass substructures. The results presented here represent the first step on the road to seeing the molecular content of the Milky Way as a forest rather than individual nearby trees.
From Peptides to Proteins: Systematic Control of Net Molecular Charge and Hydrophilicity on the Kinetics of Calcite Growth

NASA Astrophysics Data System (ADS)

Elhadj, S.; de Yoreo, J. J.; Hoyer, J. J.; Dove, P. M.

2006-12-01

The compartment-specific compositions of biologic molecules isolated from biominerals suggest that control of mineral growth may be linked to biochemical features. Here we define a systematic relationship between the ability of biomolecules in solution to promote the growth of calcite (CaCO3) and their net negative molecular charge and hydrophilicity. The degree of enhancement is dependent on peptide composition, but not on peptide sequence. Data analysis shows that this rate enhancement arises from an increase in the kinetic coefficient. We interpret the mechanism of growth enhancement to be a catalytic process whereby biomolecules reduce the magnitude of the diffusive barrier, Ek, by perturbations that displace water molecules- a water shell destruction mechanism. The result is a decrease in the repulsive barrier for attachment of solutes to the solid phase. This previously unrecognized relationship also rationalizes recently reported data showing acceleration of calcite growth rates over rates measured in the pure system by nanomolar levels of abalone nacre proteins. These findings show that the growth-modifying properties of small model peptides may be scaled up to analyze mineralization processes that are mediated by more complex proteins. We suggest that enhancement of calcite growth may now be estimated a priori from the composition of peptide sequences and the calculated values of hydrophilicity and net molecular charge without need for detailed tests for each biomolecule. This insight may contribute to an improved understanding of mineralization in diverse systems of biomineralization.
Regular Nanoscale Protein Patterns via Directed Adsorption through Self-Assembled DNA Origami Masks.

PubMed

Ramakrishnan, Saminathan; Subramaniam, Sivaraman; Stewart, A Francis; Grundmeier, Guido; Keller, Adrian

2016-11-16

DNA origami has become a widely used method for synthesizing well-defined nanostructures with promising applications in various areas of nanotechnology, biophysics, and medicine. Recently, the possibility to transfer the shape of single DNA origami nanostructures into different materials via molecular lithography approaches has received growing interest due to the great structural control provided by the DNA origami technique. Here, we use ordered monolayers of DNA origami nanostructures with internal cavities on mica surfaces as molecular lithography masks for the fabrication of regular protein patterns over large surface areas. Exposure of the masked sample surface to negatively charged proteins results in the directed adsorption of the proteins onto the exposed surface areas in the holes of the mask. By controlling the buffer and adsorption conditions, the protein coverage of the exposed areas can be varied from single proteins to densely packed monolayers. To demonstrate the versatility of this approach, regular nanopatterns of four different proteins are fabricated: the single-strand annealing proteins Redβ and Sak, the iron-storage protein ferritin, and the blood protein bovine serum albumin (BSA). We furthermore demonstrate the desorption of the DNA origami mask after directed protein adsorption, which may enable the fabrication of hierarchical patterns composed of different protein species. Because selectivity in adsorption is achieved by electrostatic interactions between the proteins and the exposed surface areas, this approach may enable also the large-scale patterning of other charged molecular species or even nanoparticles.
Giant surfactants provide a versatile platform for sub-10-nm nanostructure engineering

PubMed Central

Yu, Xinfei; Yue, Kan; Hsieh, I-Fan; Li, Yiwen; Dong, Xue-Hui; Liu, Chang; Xin, Yu; Wang, Hsiao-Fang; Shi, An-Chang; Newkome, George R.; Chen, Er-Qiang; Zhang, Wen-Bin; Cheng, Stephen Z. D.

2013-01-01

The engineering of structures across different length scales is central to the design of novel materials with controlled macroscopic properties. Herein, we introduce a unique class of self-assembling materials, which are built upon shape- and volume-persistent molecular nanoparticles and other structural motifs, such as polymers, and can be viewed as a size-amplified version of the corresponding small-molecule counterparts. Among them, “giant surfactants” with precise molecular structures have been synthesized by “clicking” compact and polar molecular nanoparticles to flexible polymer tails of various composition and architecture at specific sites. Capturing the structural features of small-molecule surfactants but possessing much larger sizes, giant surfactants bridge the gap between small-molecule surfactants and block copolymers and demonstrate a duality of both materials in terms of their self-assembly behaviors. The controlled structural variations of these giant surfactants through precision synthesis further reveal that their self-assemblies are remarkably sensitive to primary chemical structures, leading to highly diverse, thermodynamically stable nanostructures with feature sizes around 10 nm or smaller in the bulk, thin-film, and solution states, as dictated by the collective physical interactions and geometric constraints. The results suggest that this class of materials provides a versatile platform for engineering nanostructures with sub-10-nm feature sizes. These findings are not only scientifically intriguing in understanding the chemical and physical principles of the self-assembly, but also technologically relevant, such as in nanopatterning technology and microelectronics. PMID:23716680
Crystalline order of a water/glycine film coadsorbed on the (104) calcite surface.

PubMed

Magdans, Uta; Torrelles, Xavier; Angermund, Klaus; Gies, Hermann; Rius, Jordi

2007-04-24

For biomineralization processes, the interaction of the surface of calcite crystals with organic molecules is of particular importance. Especially, biologically controlled biomineralization as in exoskeletons of mollusks and echinoderms, e.g., sea urchin with single-crystal-like spines and shells,1-3 requires molecular control of seed formation and growth process. So far, experiments showing the obvious influence of organic molecules on the morphology and habit of calcite crystals have demonstrated the molecular dimension of the interaction.4-7 Details of the kinetics of growth and dissolution of mineral surfaces influenced by additives are available,8,9 but other experimental data about the structure of the organic/inorganic interface on the atomic scale are rare. On the other hand, complicated organic macromolecules which are involved in biomineralization are numerous, with only a small fraction solved in structure and function so far.10-13 Therefore, model systems have to be designed to provide a basic understanding for the interaction process.14 Using grazing incidence X-ray diffraction combined with molecular modeling techniques, we show that glycine molecules order periodically on the calcite (104) face in competition with the solvent water when exposed to an aqueous solution of the most simple amino acid. In contrast to the general concept of the charge-matching fit of organic molecules on mineral surfaces,4,14 glycine is not attached to the calcite surface directly but substitutes for water molecules in the second hydration layer.
Cross-Scale Molecular Analysis of Chemical Heterogeneity in Shale Rocks

DOE PAGES

Hao, Zhao; Bechtel, Hans A.; Kneafsey, Timothy; ...

2018-02-07

The organic and mineralogical heterogeneity in shale at micrometer and nanometer spatial scales contributes to the quality of gas reserves, gas flow mechanisms and gas production. Here, we demonstrate two molecular imaging approaches based on infrared spectroscopy to obtain mineral and kerogen information at these mesoscale spatial resolutions in large-sized shale rock samples. The first method is a modified microscopic attenuated total reflectance measurement that utilizes a large germanium hemisphere combined with a focal plane array detector to rapidly capture chemical images of shale rock surfaces spanning hundreds of micrometers with micrometer spatial resolution. The second method, synchrotron infrared nano-spectroscopy,more » utilizes a metallic atomic force microscope tip to obtain chemical images of micrometer dimensions but with nanometer spatial resolution. This chemically "deconvoluted" imaging at the nano-pore scale is then used to build a machine learning model to generate a molecular distribution map across scales with a spatial span of 1000 times, which enables high-throughput geochemical characterization in greater details across the nano-pore and micro-grain scales and allows us to identify co-localization of mineral phases with chemically distinct organics and even with gas phase sorbents. Finally, this characterization is fundamental to understand mineral and organic compositions affecting the behavior of shales.« less
Cross-Scale Molecular Analysis of Chemical Heterogeneity in Shale Rocks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hao, Zhao; Bechtel, Hans A.; Kneafsey, Timothy

The organic and mineralogical heterogeneity in shale at micrometer and nanometer spatial scales contributes to the quality of gas reserves, gas flow mechanisms and gas production. Here, we demonstrate two molecular imaging approaches based on infrared spectroscopy to obtain mineral and kerogen information at these mesoscale spatial resolutions in large-sized shale rock samples. The first method is a modified microscopic attenuated total reflectance measurement that utilizes a large germanium hemisphere combined with a focal plane array detector to rapidly capture chemical images of shale rock surfaces spanning hundreds of micrometers with micrometer spatial resolution. The second method, synchrotron infrared nano-spectroscopy,more » utilizes a metallic atomic force microscope tip to obtain chemical images of micrometer dimensions but with nanometer spatial resolution. This chemically "deconvoluted" imaging at the nano-pore scale is then used to build a machine learning model to generate a molecular distribution map across scales with a spatial span of 1000 times, which enables high-throughput geochemical characterization in greater details across the nano-pore and micro-grain scales and allows us to identify co-localization of mineral phases with chemically distinct organics and even with gas phase sorbents. Finally, this characterization is fundamental to understand mineral and organic compositions affecting the behavior of shales.« less
Multiscale Analysis of Delamination of Carbon Fiber-Epoxy Laminates with Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Riddick, Jaret C.; Frankland, SJV; Gates, TS

2006-01-01

A multi-scale analysis is presented to parametrically describe the Mode I delamination of a carbon fiber/epoxy laminate. In the midplane of the laminate, carbon nanotubes are included for the purposes of selectively enhancing the fracture toughness of the laminate. To analyze carbon fiber epoxy carbon nanotube laminate, the multi-scale methodology presented here links a series of parameterizations taken at various length scales ranging from the atomistic through the micromechanical to the structural level. At the atomistic scale molecular dynamics simulations are performed in conjunction with an equivalent continuum approach to develop constitutive properties for representative volume elements of the molecular structure of components of the laminate. The molecular-level constitutive results are then used in the Mori-Tanaka micromechanics to develop bulk properties for the epoxy-carbon nanotube matrix system. In order to demonstrate a possible application of this multi-scale methodology, a double cantilever beam specimen is modeled. An existing analysis is employed which uses discrete springs to model the fiber bridging affect during delamination propagation. In the absence of empirical data or a damage mechanics model describing the effect of CNTs on fracture toughness, several tractions laws are postulated, linking CNT volume fraction to fiber bridging in a DCB specimen. Results from this demonstration are presented in terms of DCB specimen load-displacement responses.
Magnetic Tethering of Microswimmers in Microfluidic Devices

NASA Astrophysics Data System (ADS)

Chawan, Aschvin; Jana, Saikat; Ghosh, Suvojit; Jung, Sunghwan; Puri, Ishwar

2013-03-01

Exercising control over animal locomotion is well known in the macro world. In the micro-scale world, such methods require more sophistication. We magnetize Paramecium multimicronucleatum by internalization of magnetite nanoparticles coated with bovine serum albumin (BSA). This enables control of their motion in a microfluidic device using a magnetic field. Miniature permanent magnets embedded within the device are used to tether the magnetized organisms to specific locations along a micro-channel. Ciliary beatings of the microswimmer generate shear flows nearby. We apply this setup to enhance cross-stream mixing in a microfluidic device by supplementing molecular diffusion. The device is similar to an active micromixer but requires no external power sources or artificial actuators. We optically characterize the effectiveness of the mechanism in a variety of flow situations.
TURBOGEN: Computer-controlled vertically oscillating grid system for small-scale turbulence studies on plankton

NASA Astrophysics Data System (ADS)

Amato, Alberto; Fortini, Stefania; Watteaux, Romain; Diano, Marcello; Espa, Stefania; Esposito, Serena; Ferrante, Maria I.; Peters, Francesc; Iudicone, Daniele; Ribera d'Alcalà, Maurizio

2016-03-01

In recent years, there has been a renewed interest in the impact of turbulence on aquatic organisms. In response to this interest, a novel instrument has been constructed, TURBOGEN, that generates turbulence in water volumes up to 13 l. TURBOGEN is fully computer controlled, thus, allowing for a high level of reproducibility and for variations of the intensity and characteristics of turbulence during the experiment. The calibration tests, carried out by particle image velocimetry, showed TURBOGEN to be successful in generating isotropic turbulence at the typical relatively low levels of the marine environment. TURBOGEN and its sizing have been devised with the long-term scope of analyzing in detail the molecular responses of plankton to different mixing regimes, which is of great importance in both environmental and biotechnological processes.
Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor.

PubMed

Wahle, Manuel; Wriggers, Willy

2015-10-01

The modeling of large biomolecular assemblies relies on an efficient rendering of their hierarchical architecture across a wide range of spatial level of detail. We describe a paradigm shift currently under way in computer graphics towards the use of more realistic global illumination models, and we apply the so-called ambient occlusion approach to our open-source multi-scale modeling program, Sculptor. While there are many other higher quality global illumination approaches going all the way up to full GPU-accelerated ray tracing, they do not provide size-specificity of the features they shade. Ambient occlusion is an aspect of global lighting that offers great visual benefits and powerful user customization. By estimating how other molecular shape features affect the reception of light at some surface point, it effectively simulates indirect shadowing. This effect occurs between molecular surfaces that are close to each other, or in pockets such as protein or ligand binding sites. By adding ambient occlusion, large macromolecular systems look much more natural, and the perception of characteristic surface features is strongly enhanced. In this work, we present a real-time implementation of screen space ambient occlusion that delivers realistic cues about tunable spatial scale characteristics of macromolecular architecture. Heretofore, the visualization of large biomolecular systems, comprising e.g. hundreds of thousands of atoms or Mega-Dalton size electron microscopy maps, did not take into account the length scales of interest or the spatial resolution of the data. Our approach has been uniquely customized with shading that is tuned for pockets and cavities of a user-defined size, making it useful for visualizing molecular features at multiple scales of interest. This is a feature that none of the conventional ambient occlusion approaches provide. Actual Sculptor screen shots illustrate how our implementation supports the size-dependent rendering of molecular surface features.
Layer-by-Layer Enabled Nanomaterials for Chemical Sensing and Energy Conversion

NASA Astrophysics Data System (ADS)

Paterno, Leonardo G.; Soler, Maria A. G.

2013-06-01

The layer-by-layer (LbL) technique is a wet chemical method for the assembly of ultrathin films, with thicknesses up to 100 nm. This method is based on the successive transfer of molecular layers to a solid substrate that is dipped into cationic and anionic solutions in an alternating fashion. The adsorption is mainly driven by electrostatic interactions so that many molecular and nanomaterial systems can be engineered under this method. Moreover, it is inexpensive, can be easily performed, and does not demand sophisticated equipment or clean rooms. The most explored use of the LbL technique is to build up molecular devices for chemical sensing and energy conversion. Both applications require ultrathin films where specific elements must be organized with high control of thickness and spatial distribution, preferably in the nanolength and mesolength scales. In chemical sensors, the LbL technique is employed to assemble specific sensoactive materials such as conjugated polymers, enzymes, and immunological elements onto appropriated electrodes. Molecular recognition events are thus transduced by the assembled sensoactive layer. In energy-conversion devices, the LbL technique can be employed to fabricate different device's parts including electrodes, active layers, and auxiliary layers. In both applications, the devices' performance can be fully modulated and improved by simply varying film thickness and molecular architecture. The present review article highlights the main features of the LbL technique and provides a brief description of different (bio)chemical sensors, solar cells, and organic light-emitting diodes enabled by the LbL approach.
Gears Based on Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Jaffe, Richard; Han, Jie; Globus, Al; Deardorff, Glenn

2005-01-01

Gears based on carbon nanotubes (see figure) have been proposed as components of an emerging generation of molecular- scale machines and sensors. In comparison with previously proposed nanogears based on diamondoid and fullerene molecules, the nanotube-based gears would have simpler structures and are more likely to be realizable by practical fabrication processes. The impetus for the practical development of carbon-nanotube- based gears arises, in part, from rapid recent progress in the fabrication of carbon nanotubes with prescribed diameters, lengths, chiralities, and numbers of concentric shells. The shafts of the proposed gears would be made from multiwalled carbon nanotubes. The gear teeth would be rigid molecules (typically, benzyne molecules), bonded to the nanotube shafts at atomically precise positions. For fabrication, it may be possible to position the molecular teeth by use of scanning tunneling microscopy (STM) or other related techniques. The capability to position individual organic molecules at room temperature by use of an STM tip has already been demonstrated. Routes to the chemical synthesis of carbon-nanotube-based gears are also under investigation. Chemical and physical aspects of the synthesis of molecular scale gears based on carbon nanotubes and related molecules, and dynamical properties of nanotube- based gears, have been investigated by computational simulations using established methods of quantum chemistry and molecular dynamics. Several particularly interesting and useful conclusions have been drawn from the dynamical simulations performed thus far: The forces acting on the gears would be more sensitive to local molecular motions than to gross mechanical motions of the overall gears. Although no breakage of teeth or of chemical bonds is expected at temperatures up to at least 3,000 K, the gears would not work well at temperatures above a critical range from about 600 to about 1,000 K. Gear temperature could probably be controlled by use of coolant gases. For a given application, the gears would work well at temperatures below the critical range, provided that the rotational energy was less than the energy required to tilt the teeth through an angle of 20 . The predominant mechanism of gear failure would be slippage caused by tilting of teeth. Gears would resume functioning if the slipping gears were decelerated sufficiently.
Engineering challenges for instrumenting and controlling integrated organ-on-chip systems.

PubMed

Wikswo, John P; Block, Frank E; Cliffel, David E; Goodwin, Cody R; Marasco, Christina C; Markov, Dmitry A; McLean, David L; McLean, John A; McKenzie, Jennifer R; Reiserer, Ronald S; Samson, Philip C; Schaffer, David K; Seale, Kevin T; Sherrod, Stacy D

2013-03-01

The sophistication and success of recently reported microfabricated organs-on-chips and human organ constructs have made it possible to design scaled and interconnected organ systems that may significantly augment the current drug development pipeline and lead to advances in systems biology. Physiologically realistic live microHuman (μHu) and milliHuman (mHu) systems operating for weeks to months present exciting and important engineering challenges such as determining the appropriate size for each organ to ensure appropriate relative organ functional activity, achieving appropriate cell density, providing the requisite universal perfusion media, sensing the breadth of physiological responses, and maintaining stable control of the entire system, while maintaining fluid scaling that consists of ~5 mL for the mHu and ~5 μL for the μHu. We believe that successful mHu and μHu systems for drug development and systems biology will require low-volume microdevices that support chemical signaling, microfabricated pumps, valves and microformulators, automated optical microscopy, electrochemical sensors for rapid metabolic assessment, ion mobility-mass spectrometry for real-time molecular analysis, advanced bioinformatics, and machine learning algorithms for automated model inference and integrated electronic control. Toward this goal, we are building functional prototype components and are working toward top-down system integration.

Formation and growth mechanisms of single-walled metal oxide nanotubes

NASA Astrophysics Data System (ADS)

Yucelen, Gulfem Ipek

In this thesis, main objectives are to discover the first molecular-level mechanistic framework governing the formation and growth of single-walled metal-oxide nanotubes, apply this framework to demonstrate the engineering of nanotubular materials of controlled dimensions, and to progress towards a quantitative multiscale understanding of nanotube formation. In Chapter 2, the identification and elucidation of the mechanistic role of molecular precursors and nanoscale (1-3 nm) intermediates with intrinsic curvature, in the formation of single-walled aluminosilicate nanotubes is reported. The structural and compositional evolution of molecular and nanoscale species over a length scale of 0.1-100 nm, are characterized by electrospray ionization (ESI) mass spectrometry, and nuclear magnetic resonance (NMR) spectroscopy. DFT calculations revealed the intrinsic curvature of nanoscale intermediates with bonding environments similar to the structure of the final nanotube product. It is shown that curved nano-intermediates form in aqueous synthesis solutions immediately after initial hydrolysis of reactants at 25 °C, disappear from the solution upon heating to 95 °C due to condensation, and finally rearrange to form ordered single-walled aluminosilicate nanotubes. Integration of all results leads to the construction of the first molecular-level mechanism of single-walled metal oxide nanotube formation, incorporating the role of monomeric and polymeric aluminosilicate species as well as larger nanoparticles. Then, in Chapter 3, new molecular-level concepts for constructing nanoscopic metal oxide objects are demonstrated. The diameters of metal oxide nanotubes are shaped with Angstrom-level precision by controlling the shape of nanometer-scale precursors. The subtle relationships between precursor shape and structure and final nanotube curvature are measured (at the molecular level). Anionic ligands (both organic and inorganic) are used to exert fine control over precursor shapes, allowing assembly into nanotubes whose diameters relate directly to the curvatures of shaped precursors. Having obtained considerable insight into aluminosilicate nanotube formation, in Chapter 4 the complex aqueous chemistry of nanotube-forming aluminogermanate solutions are examined. The aluminogermanate system is particularly interesting since it forms ultra-short nanotubes of lengths as small as ˜20 nm. Insights into the underlying important mechanistic differences between aluminogermanate and aluminosilicate nanotube growth as well as structural differences in the final nanotube dimensions are provided. Furthermore, an experimental example of control over nanotube length is shown, using the understanding of the mechanistic differences, along with further suggestions for possible ways of controlling nanotube lengths. In Chapter 5, a generalized kinetic model is formulated to describe the reactions leading to formation and growth of single-walled metal oxide nanotubes. This model is capable of explaining and predicting the evolution of nanotube populations as a function of kinetic parameters. It also allows considerable insight into meso/microscale nanotube growth processes. For example, it shows that two different mechanisms operate during nanotube growth: (1) growth by precursor addition, and (2) by oriented attachment of nanotubes to each other. In Chapter 6, a study of the structure of the nanotube walls is presented. A detailed investigation of the defect structures in aluminosilicate single-walled nanotubes via multiple advanced solid-state NMR techniques is reported. A combination of 1H-29Si and 1H- 27Al FSLG-HETCOR, 1H CRAMPS, and 1H- 29Si CP/MAS NMR experiments were employed to evaluate the proton environments around Al and Si atoms during nanotube synthesis and in the final structure. The HETCOR experiments allowed to track the evolving Si and Al environments during the formation of the nanotubes from precursor species, and relate them to the Si and Al coordination environments found in the final nanotube structure. (Abstract shortened by UMI.).
Bridging the physical scales in evolutionary biology: From protein sequence space to fitness of organisms and populations

PubMed Central

Bershtein, Shimon; Serohijos, Adrian W.R.; Shakhnovich, Eugene I.

2016-01-01

Bridging the gap between the molecular properties of proteins and organismal/population fitness is essential for understanding evolutionary processes. This task requires the integration of the several physical scales of biological organization, each defined by a distinct set of mechanisms and constraints, into a single unifying model. The molecular scale is dominated by the constraints imposed by the physico-chemical properties of proteins and their substrates, which give rise to trade-offs and epistatic (non-additive) effects of mutations. At the systems scale, biological networks modulate protein expression and can either buffer or enhance the fitness effects of mutations. The population scale is influenced by the mutational input, selection regimes, and stochastic changes affecting the size and structure of populations, which eventually determine the evolutionary fate of mutations. Here, we summarize the recent advances in theory, computer simulations, and experiments that advance our understanding of the links between various physical scales in biology. PMID:27810574
Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations.

PubMed

Bershtein, Shimon; Serohijos, Adrian Wr; Shakhnovich, Eugene I

2017-02-01

Bridging the gap between the molecular properties of proteins and organismal/population fitness is essential for understanding evolutionary processes. This task requires the integration of the several physical scales of biological organization, each defined by a distinct set of mechanisms and constraints, into a single unifying model. The molecular scale is dominated by the constraints imposed by the physico-chemical properties of proteins and their substrates, which give rise to trade-offs and epistatic (non-additive) effects of mutations. At the systems scale, biological networks modulate protein expression and can either buffer or enhance the fitness effects of mutations. The population scale is influenced by the mutational input, selection regimes, and stochastic changes affecting the size and structure of populations, which eventually determine the evolutionary fate of mutations. Here, we summarize the recent advances in theory, computer simulations, and experiments that advance our understanding of the links between various physical scales in biology. Copyright © 2016 Elsevier Ltd. All rights reserved.
DNA Based Molecular Scale Nanofabrication

DTIC Science & Technology

2015-12-04

structure. We developed a method to produce nanoscale patterns on SAM. (d) Studied the molecular imprinting of DNA origami structure using polymer...to produce nanoscale patterns on SAM. (d) Studied the molecular imprinting of DNA origami structure using polymer substrates. Developed a high... imprinting using DNA nanostructure templates. Soft lithography uses polymeric stamps with certain features to transfer the pattern for printing
Molecular Electronic Shift Registers

NASA Technical Reports Server (NTRS)

Beratan, David N.; Onuchic, Jose N.

1990-01-01

Molecular-scale shift registers eventually constructed as parts of high-density integrated memory circuits. In principle, variety of organic molecules makes possible large number of different configurations and modes of operation for such shift-register devices. Several classes of devices and implementations in some specific types of molecules proposed. All based on transfer of electrons or holes along chains of repeating molecular units.
Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine.

PubMed

Dudley, Joel T; Listgarten, Jennifer; Stegle, Oliver; Brenner, Steven E; Parts, Leopold

2015-01-01

Advances in molecular profiling and sensor technologies are expanding the scope of personalized medicine beyond genotypes, providing new opportunities for developing richer and more dynamic multi-scale models of individual health. Recent studies demonstrate the value of scoring high-dimensional microbiome, immune, and metabolic traits from individuals to inform personalized medicine. Efforts to integrate multiple dimensions of clinical and molecular data towards predictive multi-scale models of individual health and wellness are already underway. Improved methods for mining and discovery of clinical phenotypes from electronic medical records and technological developments in wearable sensor technologies present new opportunities for mapping and exploring the critical yet poorly characterized "phenome" and "envirome" dimensions of personalized medicine. There are ambitious new projects underway to collect multi-scale molecular, sensor, clinical, behavioral, and environmental data streams from large population cohorts longitudinally to enable more comprehensive and dynamic models of individual biology and personalized health. Personalized medicine stands to benefit from inclusion of rich new sources and dimensions of data. However, realizing these improvements in care relies upon novel informatics methodologies, tools, and systems to make full use of these data to advance both the science and translational applications of personalized medicine.
Future of Electron Scattering and Diffraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hall, Ernest; Stemmer, Susanne; Zheng, Haimei

2014-02-25

The ability to correlate the atomic- and nanoscale-structure of condensed matter with physical properties (e.g., mechanical, electrical, catalytic, and optical) and functionality forms the core of many disciplines. Directing and controlling materials at the quantum-, atomic-, and molecular-levels creates enormous challenges and opportunities across a wide spectrum of critical technologies, including those involving the generation and use of energy. The workshop identified next generation electron scattering and diffraction instruments that are uniquely positioned to address these grand challenges. The workshop participants identified four key areas where the next generation of such instrumentation would have major impact: A – Multidimensional Visualizationmore » of Real Materials B – Atomic-scale Molecular Processes C – Photonic Control of Emergence in Quantum Materials D – Evolving Interfaces, Nucleation, and Mass Transport Real materials are comprised of complex three-dimensional arrangements of atoms and defects that directly determine their potential for energy applications. Understanding real materials requires new capabilities for three-dimensional atomic scale tomography and spectroscopy of atomic and electronic structures with unprecedented sensitivity, and with simultaneous spatial and energy resolution. Many molecules are able to selectively and efficiently convert sunlight into other forms of energy, like heat and electric current, or store it in altered chemical bonds. Understanding and controlling such process at the atomic scale require unprecedented time resolution. One of the grand challenges in condensed matter physics is to understand, and ultimately control, emergent phenomena in novel quantum materials that necessitate developing a new generation of instruments that probe the interplay among spin, charge, orbital, and lattice degrees of freedom with intrinsic time- and length-scale resolutions. Molecules and soft matter require imaging and spectroscopy with high spatial resolution without damaging their structure. The strong interaction of electrons with matter allows high-energy electron pulses to gather structural information before a sample is damaged. Electron ScatteringImaging, diffraction, and spectroscopy are the fundamental capabilities of electron-scattering instruments. The DOE BES-funded TEAM (Transmission Electron Aberration-corrected Microscope) project achieved unprecedented sub-atomic spatial resolution in imaging through aberration-corrected transmission electron microscopy. To further advance electron scattering techniques that directly enable groundbreaking science, instrumentation must advance beyond traditional two-dimensional imaging. Advances in temporal resolution, recording the full phase and energy spaces, and improved spatial resolution constitute a new frontier in electron microscopy, and will directly address the BES Grand Challenges, such as to “control the emergent properties that arise from the complex correlations of atomic and electronic constituents” and the “hidden states” “very far away from equilibrium”. Ultrafast methods, such as the pump-probe approach, enable pathways toward understanding, and ultimately controlling, the chemical dynamics of molecular systems and the evolution of complexity in mesoscale and nanoscale systems. Central to understanding how to synthesize and exploit functional materials is having the ability to apply external stimuli (such as heat, light, a reactive flux, and an electrical bias) and to observe the resulting dynamic process in situ and in operando, and under the appropriate environment (e.g., not limited to UHV conditions). To enable revolutionary advances in electron scattering and science, the participants of the workshop recommended three major new instrumental developments: A. Atomic-Resolution Multi-Dimensional Transmission Electron Microscope: This instrument would provide quantitative information over the entire real space, momentum space, and energy space for visualizing dopants, interstitials, and light elements; for imaging localized vibrational modes and the motion of charged particles and vacancies; for correlating lattice, spin, orbital, and charge; and for determining the structure and molecular chemistry of organic and soft matter. The instrument will be uniquely suited to answer fundamental questions in condensed matter physics that require understanding the physical and electronic structure at the atomic scale. Key developments include stable cryogenic capabilities that will allow access to emergent electronic phases, as well as hard/soft interfaces and radiation- sensitive materials. B. Ultrafast Electron Diffraction and Microscopy Instrument: This instrument would be capable of nano-diffraction with 10 fs temporal resolution in stroboscopic mode, and better than 100 fs temporal resolution in single shot mode. The instrument would also achieve single- shot real-space imaging with a spatial/temporal resolution of 10 nm/10 ps, representing a thousand fold improvement over current microscopes. Such a capability would be complementary to x-ray free electron lasers due to the difference in the nature of electron and x-ray scattering, enabling space-time mapping of lattice vibrations and energy transport, facilitating the understanding of molecular dynamics of chemical reactions, the photonic control of emergence in quantum materials, and the dynamics of mesoscopic materials. C. Lab-In-Gap Dynamic Microscope: This instrument would enable quantitative measurements of materials structure, composition, and bonding evolution in technologically relevant environments, including liquids, gases and plasmas, thereby assuring the understanding of structure function relationship at the atomic scale with up to nanosecond temporal resolution. This instrument would employ a versatile, modular sample stage and holder geometry to allow the multi-modal (e.g., optical, thermal, mechanical, electrical, and electrochemical) probing of materials’ functionality in situ and in operando. The electron optics encompasses a pole piece that can accommodate the new stage, differential pumping, detectors, aberration correctors, and other electron optical elements for measurement of materials dynamics. To realize the proposed instruments in a timely fashion, BES should aggressively support research and development of complementary and enabling instruments, including new electron sources, advanced electron optics, new tunable specimen pumps and sample stages, and new detectors. The proposed instruments would have transformative impact on physics, chemistry, materials science, engineering« less
Particle-scale measurement of PAH aqueous equilibrium partitioning in impacted sediments.

PubMed

Ghosh, Upal; Hawthorne, Steven B

2010-02-15

This research investigated the particle-scale processes that control aqueous equilibrium partitioning of PAHs in manufactured gas plant (MGP) site sediments. Dominant particle types in impacted sediments (sand, wood, coal/coke, and pitch) were physically separated under a microscope for equilibrium assessments. Solid-phase microextraction (SPME) combined with selected ion monitoring GC/MS and perdeuterated PAH internal standards were used to determine freely dissolved PAH concentrations in small (0.1-1 mL) water samples at concentrations as low as microg/L (for lower molecular weight PAHs) to ng/L (for higher molecular weight PAHs). For every particle class the initial release of PAHs into the aqueous phase was rapid, and an apparent equilibrium was reached in a matter of days. The average ratio of aqueous total PAH concentration for pitch vs coal/coke particles for eight sediment samples was 20. Thus, sediments that had aged in the field for many decades were not at equilibrium and were still going through a slow process of contaminant mass transfer between the different particle types. A possible consequence of this slow aging process is further lowering of the activity of the chemical as mass transfer is achieved to new sorption sites with time. This study also found that the presence of black carbon even at the level of (1)/(3) of sediment organic carbon does not necessarily imply a BC-dominated sorption behavior, rather source pitch particles if present may dominate PAH partitioning. To our knowledge this is the first report of equilibrium partitioning assessment conducted at the sediment particle scale.
Breakthrough and future: nanoscale controls of compositions, morphologies, and mesochannel orientations toward advanced mesoporous materials.

PubMed

Yamauchi, Yusuke; Suzuki, Norihiro; Radhakrishnan, Logudurai; Wang, Liang

2009-01-01

Currently, ordered mesoporous materials prepared through the self-assembly of surfactants have attracted growing interests owing to their special properties, including uniform mesopores and a high specific surface area. Here we focus on fine controls of compositions, morphologies, mesochannel orientations which are important factors for design of mesoporous materials with new functionalities. This Review describes our recent progress toward advanced mesoporous materials. Mesoporous materials now include a variety of inorganic-based materials, for example, transition-metal oxides, carbons, inorganic-organic hybrid materials, polymers, and even metals. Mesoporous metals with metallic frameworks can be produced by using surfactant-based synthesis with electrochemical methods. Owing to their metallic frameworks, mesoporous metals with high electroconductivity and high surface areas hold promise for a wide range of potential applications, such as electronic devices, magnetic recording media, and metal catalysts. Fabrication of mesoporous materials with controllable morphologies is also one of the main subjects in this rapidly developing research field. Mesoporous materials in the form of films, spheres, fibers, and tubes have been obtained by various synthetic processes such as evaporation-mediated direct templating (EDIT), spray-dried techniques, and collaboration with hard-templates such as porous anodic alumina and polymer membranes. Furthermore, we have developed several approaches for orientation controls of 1D mesochannels. The macroscopic-scale controls of mesochannels are important for innovative applications such as molecular-scale devices and electrodes with enhanced diffusions of guest species. Copyright 2009 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.
Microsatellites Reveal a High Population Structure in Triatoma infestans from Chuquisaca, Bolivia

PubMed Central

Pizarro, Juan Carlos; Gilligan, Lauren M.; Stevens, Lori

2008-01-01

Background For Chagas disease, the most serious infectious disease in the Americas, effective disease control depends on elimination of vectors through spraying with insecticides. Molecular genetic research can help vector control programs by identifying and characterizing vector populations and then developing effective intervention strategies. Methods and Findings The population genetic structure of Triatoma infestans (Hemiptera: Reduviidae), the main vector of Chagas disease in Bolivia, was investigated using a hierarchical sampling strategy. A total of 230 adults and nymphs from 23 localities throughout the department of Chuquisaca in Southern Bolivia were analyzed at ten microsatellite loci. Population structure, estimated using analysis of molecular variance (AMOVA) to estimate FST (infinite alleles model) and RST (stepwise mutation model), was significant between western and eastern regions within Chuquisaca and between insects collected in domestic and peri-domestic habitats. Genetic differentiation at three different hierarchical geographic levels was significant, even in the case of adjacent households within a single locality (R ST = 0.14, F ST = 0.07). On the largest geographic scale, among five communities up to 100 km apart, R ST = 0.12 and F ST = 0.06. Cluster analysis combined with assignment tests identified five clusters within the five communities. Conclusions Some houses are colonized by insects from several genetic clusters after spraying, whereas other households are colonized predominately by insects from a single cluster. Significant population structure, measured by both R ST and F ST, supports the hypothesis of poor dispersal ability and/or reduced migration of T. infestans. The high degree of genetic structure at small geographic scales, inferences from cluster analysis and assignment tests, and demographic data suggest reinfesting vectors are coming from nearby and from recrudescence (hatching of eggs that were laid before insecticide spraying). Suggestions for using these results in vector control strategies are made. PMID:18365033
The posttraumatic stress disorder project in Brazil: neuropsychological, structural and molecular neuroimaging studies in victims of urban violence.

PubMed

Bressan, Rodrigo A; Quarantini, Lucas C; Andreoli, Sérgio B; Araújo, Celia; Breen, Gerome; Guindalini, Camila; Hoexter, Marcelo; Jackowski, Andrea P; Jorge, Miguel R; Lacerda, Acioly L T; Lara, Diogo R; Malta, Stella; Moriyama, Tais S; Quintana, Maria I; Ribeiro, Wagner S; Ruiz, Juliana; Schoedl, Aline F; Shih, Ming C; Figueira, Ivan; Koenen, Karestan C; Mello, Marcelo F; Mari, Jair J

2009-06-01

Life trauma is highly prevalent in the general population and posttraumatic stress disorder is among the most prevalent psychiatric consequences of trauma exposure. Brazil has a unique environment to conduct translational research about psychological trauma and posttraumatic stress disorder, since urban violence became a Brazilian phenomenon, being particularly related to the rapid population growth of its cities. This research involves three case-control studies: a neuropsychological, a structural neuroimaging and a molecular neuroimaging study, each focusing on different objectives but providing complementary information. First, it aims to examine cognitive functioning of PTSD subjects and its relationships with symptomatology. The second objective is to evaluate neurostructural integrity of orbitofrontal cortex and hippocampus in PTSD subjects. The third aim is to evaluate if patients with PTSD have decreased dopamine transporter density in the basal ganglia as compared to resilient controls subjects. This paper shows the research rationale and design for these three case-control studies. Cases and controls will be identified through an epidemiologic survey conducted in the city of São Paulo. Subjects exposed to traumatic life experiences resulting in posttraumatic stress disorder (cases) will be compared to resilient victims of traumatic life experiences without PTSD (controls) aiming to identify biological variables that might protect or predispose to PTSD. In the neuropsychological case-control study, 100 patients with PTSD, will be compared with 100 victims of trauma without posttraumatic stress disorder, age- and sex-matched controls. Similarly, 50 cases and 50 controls will be enrolled for the structural study and 25 cases and 25 controls in the functional neuroimaging study. All individuals from the three studies will complete psychometrics and a structured clinical interview (the Structured Clinical Interview for DSM-IV and the Clinician-Administered PTSD Scale, Beck Anxiety Inventory, Beck Depression Inventory, Global Assessment of Function, The Social Adjustment Scale, Medical Outcomes Study 36-Item Short-Form Health Survey, Early Trauma Inventory, Clinical global Impressions, and Peritraumatic Dissociative Experiences Questionnaire). A broad neuropsychological battery will be administered for all participants of the neuropsychological study. Magnetic resonance scans will be performed to acquire structural neuroimaging data. Single photon emission computerized tomography with [(99m)Tc]-TRODAT-1 brain scans will be performed to evaluate dopamine transporters. This study protocol will be informative for researchers and clinicians interested in considering, designing and/or conducting translational research in the field of trauma and posttraumatic stress disorder.
Atomistic details of protein dynamics and the role of hydration water

DOE PAGES

Khodadadi, Sheila; Sokolov, Alexei P.

2016-05-04

The importance of protein dynamics for their biological activity is nowwell recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. But, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited. Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes. Internal protein dynamics spread overmore » a wide time range fromfaster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10 100 ps time scale. Our process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape.« less
Growing Out of Stress: The Role of Cell- and Organ-Scale Growth Control in Plant Water-Stress Responses[OPEN

PubMed Central

Robbins, Neil E.

2016-01-01

Water is the most limiting resource on land for plant growth, and its uptake by plants is affected by many abiotic stresses, such as salinity, cold, heat, and drought. While much research has focused on exploring the molecular mechanisms underlying the cellular signaling events governing water-stress responses, it is also important to consider the role organismal structure plays as a context for such responses. The regulation of growth in plants occurs at two spatial scales: the cell and the organ. In this review, we focus on how the regulation of growth at these different spatial scales enables plants to acclimate to water-deficit stress. The cell wall is discussed with respect to how the physical properties of this structure affect water loss and how regulatory mechanisms that affect wall extensibility maintain growth under water deficit. At a higher spatial scale, the architecture of the root system represents a highly dynamic physical network that facilitates access of the plant to a heterogeneous distribution of water in soil. We discuss the role differential growth plays in shaping the structure of this system and the physiological implications of such changes. PMID:27503468
Atomistic details of protein dynamics and the role of hydration water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khodadadi, Sheila; Sokolov, Alexei P.

The importance of protein dynamics for their biological activity is nowwell recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. But, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited. Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes. Internal protein dynamics spread overmore » a wide time range fromfaster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10 100 ps time scale. Our process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape.« less
Molecular dynamics on diffusive time scales from the phase-field-crystal equation.

PubMed

Chan, Pak Yuen; Goldenfeld, Nigel; Dantzig, Jon

2009-03-01

We extend the phase-field-crystal model to accommodate exact atomic configurations and vacancies by requiring the order parameter to be non-negative. The resulting theory dictates the number of atoms and describes the motion of each of them. By solving the dynamical equation of the model, which is a partial differential equation, we are essentially performing molecular dynamics simulations on diffusive time scales. To illustrate this approach, we calculate the two-point correlation function of a fluid.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Elber, Ron

Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances.
Endogenous Bioelectric Signaling Networks: Exploiting Voltage Gradients for Control of Growth and Form.

PubMed

Levin, Michael; Pezzulo, Giovanni; Finkelstein, Joshua M

2017-06-21

Living systems exhibit remarkable abilities to self-assemble, regenerate, and remodel complex shapes. How cellular networks construct and repair specific anatomical outcomes is an open question at the heart of the next-generation science of bioengineering. Developmental bioelectricity is an exciting emerging discipline that exploits endogenous bioelectric signaling among many cell types to regulate pattern formation. We provide a brief overview of this field, review recent data in which bioelectricity is used to control patterning in a range of model systems, and describe the molecular tools being used to probe the role of bioelectrics in the dynamic control of complex anatomy. We suggest that quantitative strategies recently developed to infer semantic content and information processing from ionic activity in the brain might provide important clues to cracking the bioelectric code. Gaining control of the mechanisms by which large-scale shape is regulated in vivo will drive transformative advances in bioengineering, regenerative medicine, and synthetic morphology, and could be used to therapeutically address birth defects, traumatic injury, and cancer.
LAD Dissertation Prize Talk: Molecular Collisional Excitation in Astrophysical Environments

NASA Astrophysics Data System (ADS)

Walker, Kyle M.

2017-06-01

While molecular excitation calculations are vital in determining particle velocity distributions, internal state distributions, abundances, and ionization balance in gaseous environments, both theoretical calculations and experimental data for these processes are lacking. Reliable molecular collisional data with the most abundant species - H2, H, He, and electrons - are needed to probe material in astrophysical environments such as nebulae, molecular clouds, comets, and planetary atmospheres. However, excitation calculations with the main collider, H2, are computationally expensive and therefore various approximations are used to obtain unknown rate coefficients. The widely-accepted collider-mass scaling approach is flawed, and alternate scaling techniques based on physical and mathematical principles are presented here. The most up-to-date excitation data are used to model the chemical evolution of primordial species in the Recombination Era and produce accurate non-thermal spectra of the molecules H2+, HD, and H2 in a primordial cloud as it collapses into a first generation star.
A Langevin model for fluctuating contact angle behaviour parametrised using molecular dynamics.

PubMed

Smith, E R; Müller, E A; Craster, R V; Matar, O K

2016-12-06

Molecular dynamics simulations are employed to develop a theoretical model to predict the fluid-solid contact angle as a function of wall-sliding speed incorporating thermal fluctuations. A liquid bridge between counter-sliding walls is studied, with liquid-vapour interface-tracking, to explore the impact of wall-sliding speed on contact angle. The behaviour of the macroscopic contact angle varies linearly over a range of capillary numbers beyond which the liquid bridge pinches off, a behaviour supported by experimental results. Nonetheless, the liquid bridge provides an ideal test case to study molecular scale thermal fluctuations, which are shown to be well described by Gaussian distributions. A Langevin model for contact angle is parametrised to incorporate the mean, fluctuation and auto-correlations over a range of sliding speeds and temperatures. The resulting equations can be used as a proxy for the fully-detailed molecular dynamics simulation allowing them to be integrated within a continuum-scale solver.
Molecular clouds and the large-scale structure of the galaxy

NASA Technical Reports Server (NTRS)

Thaddeus, Patrick; Stacy, J. Gregory

1990-01-01

The application of molecular radio astronomy to the study of the large-scale structure of the Galaxy is reviewed and the distribution and characteristic properties of the Galactic population of Giant Molecular Clouds (GMCs), derived primarily from analysis of the Columbia CO survey, and their relation to tracers of Population 1 and major spiral features are described. The properties of the local molecular interstellar gas are summarized. The CO observing programs currently underway with the Center for Astrophysics 1.2 m radio telescope are described, with an emphasis on projects relevant to future comparison with high-energy gamma-ray observations. Several areas are discussed in which high-energy gamma-ray observations by the EGRET (Energetic Gamma-Ray Experiment Telescope) experiment aboard the Gamma Ray Observatory will directly complement radio studies of the Milky Way, with the prospect of significant progress on fundamental issues related to the structure and content of the Galaxy.

Molecular-scale properties of MoO3 -doped pentacene

NASA Astrophysics Data System (ADS)

Ha, Sieu D.; Meyer, Jens; Kahn, Antoine

2010-10-01

The mechanisms of molecular doping in organic electronic materials are explored through investigation of pentacene p -doped with molybdenum trioxide (MoO3) . Doping is confirmed with ultraviolet photoelectron spectroscopy. Isolated dopants are imaged at the molecular scale using scanning tunneling microscopy (STM) and effects due to localized holes are observed. The results demonstrate that donated charges are localized by the counterpotential of ionized dopants in MoO3 -doped pentacene, generalizing similar effects previously observed for pentacene doped with tetrafluoro-tetracyanoquinodimethane. Such localized hole effects are only observed for low molecular weight MoO3 species. It is shown that for larger MoO3 polymers and clusters, the ionized dopant potential is sufficiently large as to mask the effect of the localized hole in STM images. Current-voltage measurements recorded using scanning tunneling spectroscopy reveal that electron conductivity decreases in MoO3 -doped films, as expected for electron capture and p -doping.
LAMMPS integrated materials engine (LIME) for efficient automation of particle-based simulations: application to equation of state generation

NASA Astrophysics Data System (ADS)

Barnes, Brian C.; Leiter, Kenneth W.; Becker, Richard; Knap, Jaroslaw; Brennan, John K.

2017-07-01

We describe the development, accuracy, and efficiency of an automation package for molecular simulation, the large-scale atomic/molecular massively parallel simulator (LAMMPS) integrated materials engine (LIME). Heuristics and algorithms employed for equation of state (EOS) calculation using a particle-based model of a molecular crystal, hexahydro-1,3,5-trinitro-s-triazine (RDX), are described in detail. The simulation method for the particle-based model is energy-conserving dissipative particle dynamics, but the techniques used in LIME are generally applicable to molecular dynamics simulations with a variety of particle-based models. The newly created tool set is tested through use of its EOS data in plate impact and Taylor anvil impact continuum simulations of solid RDX. The coarse-grain model results from LIME provide an approach to bridge the scales from atomistic simulations to continuum simulations.
Non-translational Molecular Diffusive Motion on Two Different Time Scales in Alkane Nanoparticles

NASA Astrophysics Data System (ADS)

Wang, S.-K.; Bai, M.; Taub, H.; Mamontov, E.; Herwig, K. W.; Hansen, F. Y.; Copley, J. R. D.; Jenkins, T.; Tyagi, M.; Volkmann, U. G.

2009-03-01

Using quasielastic neutron scattering, we have investigated molecular diffusive motion in n-C32H66 nanoparticles whose structure and phase transitions have been studied previously.^2 The spectra reveal non-translational (dispersionless) diffusive motion occurring simultaneously on time scales of ˜1 ns and ˜40 ps. The onset of the faster motion occurs in the crystalline phase at least 15 K below the melting point and is tentatively identified with rotation about the long molecular axis. Similarly, we suggest that the slower motion involves molecular conformational changes whose onset appears to coincide with the abrupt transition to the bulk rotator phase about 3 K below melting. These two types of diffusive motion bear a strong resemblance to those observed previously in C24 monolayers adsorbed on a graphite surface.^3 ^2M. Bai et al., Europhys. Lett. 79, 26003 (2007). ^3F. Y. Hansen et al., Phys. Rev. Lett. 92, 046103 (2004)].
Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation

NASA Astrophysics Data System (ADS)

Kekenes-Huskey, P. M.; Gillette, A. K.; McCammon, J. A.

2014-05-01

The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the volume excluded by solute "obstacles" and (2) long-range interactions between those obstacles and the diffuser. Increasing excluded volume reduces transport of the diffuser, while long-range interactions can either increase or decrease diffusivity, depending on the nature of the potential. We previously demonstrated [P. M. Kekenes-Huskey et al., Biophys. J. 105, 2130 (2013)] using homogenization theory that the configuration of molecular-scale obstacles can both hinder diffusion and induce diffusional anisotropy for small ions. As the density of molecular obstacles increases, van der Waals (vdW) and electrostatic interactions between obstacle and a diffuser become significant and can strongly influence the latter's diffusivity, which was neglected in our original model. Here, we extend this methodology to include a fixed (time-independent) potential of mean force, through homogenization of the Smoluchowski equation. We consider the diffusion of ions in crowded, hydrophilic environments at physiological ionic strengths and find that electrostatic and vdW interactions can enhance or depress effective diffusion rates for attractive or repulsive forces, respectively. Additionally, we show that the observed diffusion rate may be reduced independent of non-specific electrostatic and vdW interactions by treating obstacles that exhibit specific binding interactions as "buffers" that absorb free diffusers. Finally, we demonstrate that effective diffusion rates are sensitive to distribution of surface charge on a globular protein, Troponin C, suggesting that the use of molecular structures with atomistic-scale resolution can account for electrostatic influences on substrate transport. This approach offers new insight into the influence of molecular-scale, long-range interactions on transport of charged species, particularly for diffusion-influenced signaling events occurring in crowded cellular environments.
Materials by Design—A Perspective From Atoms to Structures

PubMed Central

Buehler, Markus J.

2013-01-01

Biological materials are effectively synthesized, controlled, and used for a variety of purposes—in spite of limitations in energy, quality, and quantity of their building blocks. Whereas the chemical composition of materials in the living world plays a some role in achieving functional properties, the way components are connected at different length scales defines what material properties can be achieved, how they can be altered to meet functional requirements, and how they fail in disease states and other extreme conditions. Recent work has demonstrated this by using large-scale computer simulations to predict materials properties from fundamental molecular principles, combined with experimental work and new mathematical techniques to categorize complex structure-property relationships into a systematic framework. Enabled by such categorization, we discuss opportunities based on the exploitation of concepts from distinct hierarchical systems that share common principles in how function is created, linking music to materials science. PMID:24163499
Biaxial ferromagnetic liquid crystal colloids

PubMed Central

Liu, Qingkun; Ackerman, Paul J.; Lubensky, Tom C.; Smalyukh, Ivan I.

2016-01-01

The design and practical realization of composite materials that combine fluidity and different forms of ordering at the mesoscopic scale are among the grand fundamental science challenges. These composites also hold a great potential for technological applications, ranging from information displays to metamaterials. Here we introduce a fluid with coexisting polar and biaxial ordering of organic molecular and magnetic colloidal building blocks exhibiting the lowest symmetry orientational order. Guided by interactions at different length scales, rod-like organic molecules of this fluid spontaneously orient along a direction dubbed “director,” whereas magnetic colloidal nanoplates order with their dipole moments parallel to each other but pointing at an angle to the director, yielding macroscopic magnetization at no external fields. Facile magnetic switching of such fluids is consistent with predictions of a model based on competing actions of elastic and magnetic torques, enabling previously inaccessible control of light. PMID:27601668
Endocytic reawakening of motility in jammed epithelia

NASA Astrophysics Data System (ADS)

Malinverno, Chiara; Corallino, Salvatore; Giavazzi, Fabio; Bergert, Martin; Li, Qingsen; Leoni, Marco; Disanza, Andrea; Frittoli, Emanuela; Oldani, Amanda; Martini, Emanuele; Lendenmann, Tobias; Deflorian, Gianluca; Beznoussenko, Galina V.; Poulikakos, Dimos; Ong, Kok Haur; Uroz, Marina; Trepat, Xavier; Parazzoli, Dario; Maiuri, Paolo; Yu, Weimiao; Ferrari, Aldo; Cerbino, Roberto; Scita, Giorgio

2017-05-01

Dynamics of epithelial monolayers has recently been interpreted in terms of a jamming or rigidity transition. How cells control such phase transitions is, however, unknown. Here we show that RAB5A, a key endocytic protein, is sufficient to induce large-scale, coordinated motility over tens of cells, and ballistic motion in otherwise kinetically arrested monolayers. This is linked to increased traction forces and to the extension of cell protrusions, which align with local velocity. Molecularly, impairing endocytosis, macropinocytosis or increasing fluid efflux abrogates RAB5A-induced collective motility. A simple model based on mechanical junctional tension and an active cell reorientation mechanism for the velocity of self-propelled cells identifies regimes of monolayer dynamics that explain endocytic reawakening of locomotion in terms of a combination of large-scale directed migration and local unjamming. These changes in multicellular dynamics enable collectives to migrate under physical constraints and may be exploited by tumours for interstitial dissemination.
Microsecond MD Simulations of Nano-patterned Polymer Brushes on Self-Assembled Monolayers

NASA Astrophysics Data System (ADS)

Buie, Creighton; Qiu, Liming; Cheng, Kwan; Park, Soyeun

2010-03-01

Nano-patterned polymer brushes end-grafted onto self-assembled monolayers have gained increasing research interests due to their unique thermodynamic properties and their chemical and biomedical applications in colloids, biosensing and tissue engineering. So far, the interactions between the polymer brushes with the surrounding environments such as the floor and solvent at the nanometer length scale and microsecond time scale are still difficult to obtained experimentally and computationally. Using a Coarse-Grained MD approach, polymer brushes of different monomeric lengths, grafting density and hydrophobicity of the monomers grafted on self-assembled monolayers and in explicit solvent were studied. Molecular level information, such as lateral diffusion, transverse height and volume contour of the brushes, were calculated from our microsecond-MD simulations. Our results demonstrated the significance of the hydration of the polymer in controlling the conformational arrangement of the polymer brushes.
Mechanism for starch granule ghost formation deduced from structural and enzyme digestion properties.

PubMed

Zhang, Bin; Dhital, Sushil; Flanagan, Bernadine M; Gidley, Michael J

2014-01-22

After heating in excess water under little or no shear, starch granules do not dissolve completely but persist as highly swollen fragile forms, commonly termed granule "ghosts". The macromolecular architecture of these ghosts has not been defined, despite their importance in determining characteristic properties of starches. In this study, amylase digestion of isolated granule ghosts from maize and potato starches is used as a probe to study the mechanism of ghost formation, through microstructural, mesoscopic, and molecular scale analyses of structure before and after digestion. Digestion profiles showed that neither integral nor surface proteins/lipids were crucial for control of either ghost digestion or integrity. On the basis of the molecular composition and conformation of enzyme-resistant fractions, it was concluded that the condensed polymeric surface structure of ghost particles is mainly composed of nonordered but entangled amylopectin (and some amylose) molecules, with limited reinforcement through partially ordered enzyme-resistant structures based on amylose (for maize starch; V-type order) or amylopectin (for potato starch; B-type order). The high level of branching and large molecular size of amylopectin is proposed to be the origin for the unusual stability of a solid structure based primarily on temporary entanglements.
Computational screening of biomolecular adsorption and self-assembly on nanoscale surfaces.

PubMed

Heinz, Hendrik

2010-05-01

The quantification of binding properties of ions, surfactants, biopolymers, and other macromolecules to nanometer-scale surfaces is often difficult experimentally and a recurring challenge in molecular simulation. A simple and computationally efficient method is introduced to compute quantitatively the energy of adsorption of solute molecules on a given surface. Highly accurate summation of Coulomb energies as well as precise control of temperature and pressure is required to extract the small energy differences in complex environments characterized by a large total energy. The method involves the simulation of four systems, the surface-solute-solvent system, the solute-solvent system, the solvent system, and the surface-solvent system under consideration of equal molecular volumes of each component under NVT conditions using standard molecular dynamics or Monte Carlo algorithms. Particularly in chemically detailed systems including thousands of explicit solvent molecules and specific concentrations of ions and organic solutes, the method takes into account the effect of complex nonbond interactions and rotational isomeric states on the adsorption behavior on surfaces. As a numerical example, the adsorption of a dodecapeptide on the Au {111} and mica {001} surfaces is described in aqueous solution. Copyright 2009 Wiley Periodicals, Inc.
High pressure homogenization to improve the stability of casein - hydroxypropyl cellulose aqueous systems.

PubMed

Ye, Ran; Harte, Federico

2014-03-01

The effect of high pressure homogenization on the improvement of the stability hydroxypropyl cellulose (HPC) and micellar casein was investigated. HPC with two molecular weights (80 and 1150 kDa) and micellar casein were mixed in water to a concentration leading to phase separation (0.45% w/v HPC and 3% w/v casein) and immediately subjected to high pressure homogenization ranging from 0 to 300 MPa, in 100 MPa increments. The various dispersions were evaluated for stability, particle size, turbidity, protein content, and viscosity over a period of two weeks and Scanning Transmission Electron Microscopy (STEM) at the end of the storage period. The stability of casein-HPC complexes was enhanced with the increasing homogenization pressure, especially for the complex containing high molecular weight HPC. The apparent particle size of complexes was reduced from ~200nm to ~130nm when using 300 MPa, corresponding to the sharp decrease of absorbance when compared to the non-homogenized controls. High pressure homogenization reduced the viscosity of HPC-casein complexes regardless of the molecular weight of HPC and STEM imagines revealed aggregates consistent with nano-scale protein polysaccharide interactions.
High pressure homogenization to improve the stability of casein - hydroxypropyl cellulose aqueous systems

PubMed Central

Ye, Ran; Harte, Federico

2013-01-01

The effect of high pressure homogenization on the improvement of the stability hydroxypropyl cellulose (HPC) and micellar casein was investigated. HPC with two molecular weights (80 and 1150 kDa) and micellar casein were mixed in water to a concentration leading to phase separation (0.45% w/v HPC and 3% w/v casein) and immediately subjected to high pressure homogenization ranging from 0 to 300 MPa, in 100 MPa increments. The various dispersions were evaluated for stability, particle size, turbidity, protein content, and viscosity over a period of two weeks and Scanning Transmission Electron Microscopy (STEM) at the end of the storage period. The stability of casein-HPC complexes was enhanced with the increasing homogenization pressure, especially for the complex containing high molecular weight HPC. The apparent particle size of complexes was reduced from ~200nm to ~130nm when using 300 MPa, corresponding to the sharp decrease of absorbance when compared to the non-homogenized controls. High pressure homogenization reduced the viscosity of HPC-casein complexes regardless of the molecular weight of HPC and STEM imagines revealed aggregates consistent with nano-scale protein polysaccharide interactions. PMID:24159250
Length-scale dependent mechanical properties of Al-Cu eutectic alloy: Molecular dynamics based model and its experimental verification

NASA Astrophysics Data System (ADS)

Tiwary, C. S.; Chakraborty, S.; Mahapatra, D. R.; Chattopadhyay, K.

2014-05-01

This paper attempts to gain an understanding of the effect of lamellar length scale on the mechanical properties of two-phase metal-intermetallic eutectic structure. We first develop a molecular dynamics model for the in-situ grown eutectic interface followed by a model of deformation of Al-Al2Cu lamellar eutectic. Leveraging the insights obtained from the simulation on the behaviour of dislocations at different length scales of the eutectic, we present and explain the experimental results on Al-Al2Cu eutectic with various different lamellar spacing. The physics behind the mechanism is further quantified with help of atomic level energy model for different length scale as well as different strain. An atomic level energy partitioning of the lamellae and the interface regions reveals that the energy of the lamellae core are accumulated more due to dislocations irrespective of the length-scale. Whereas the energy of the interface is accumulated more due to dislocations when the length-scale is smaller, but the trend is reversed when the length-scale is large beyond a critical size of about 80 nm.
A Community Standard Format for the Representation of Protein Affinity Reagents*

PubMed Central

Gloriam, David E.; Orchard, Sandra; Bertinetti, Daniela; Björling, Erik; Bongcam-Rudloff, Erik; Borrebaeck, Carl A. K.; Bourbeillon, Julie; Bradbury, Andrew R. M.; de Daruvar, Antoine; Dübel, Stefan; Frank, Ronald; Gibson, Toby J.; Gold, Larry; Haslam, Niall; Herberg, Friedrich W.; Hiltke, Tara; Hoheisel, Jörg D.; Kerrien, Samuel; Koegl, Manfred; Konthur, Zoltán; Korn, Bernhard; Landegren, Ulf; Montecchi-Palazzi, Luisa; Palcy, Sandrine; Rodriguez, Henry; Schweinsberg, Sonja; Sievert, Volker; Stoevesandt, Oda; Taussig, Michael J.; Ueffing, Marius; Uhlén, Mathias; van der Maarel, Silvère; Wingren, Christer; Woollard, Peter; Sherman, David J.; Hermjakob, Henning

2010-01-01

Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome scale applications. This situation has triggered several initiatives involving large scale generation and validation of antibodies, for example the Swedish Human Protein Atlas and the German Antibody Factory. Antibodies targeting specific subproteomes are being pursued by members of Human Proteome Organisation (plasma and liver proteome projects) and the United States National Cancer Institute (cancer-associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality-controlled protein-binding reagents for the whole human proteome. An ultimate PAR database resource would allow consumers to visit one on-line warehouse and find all available affinity reagents from different providers together with documentation that facilitates easy comparison of their cost and quality. However, in contrast to, for example, nucleotide databases among which data are synchronized between the major data providers, current PAR producers, quality control centers, and commercial companies all use incompatible formats, hindering data exchange. Here we propose Proteomics Standards Initiative (PSI)-PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI-PAR format is maintained by the Human Proteome Organisation PSI and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI-molecular interaction, which is a widely accepted and established community standard for molecular interaction data. Further information and documentation are available on the PSI-PAR web site. PMID:19674966
South American Leaf Blight of the Rubber Tree (Hevea spp.): New Steps in Plant Domestication using Physiological Features and Molecular Markers

PubMed Central

Lieberei, Reinhard

2007-01-01

Background Rubber trees (Hevea spp.) are perennial crops of Amazonian origin that have been spread over the whole tropical belt to guarantee worldwide production of natural rubber. This crop plant has found its place in many national economies of producing countries, and although its domestication by selection of suitable genotypes was very slow, it contributes a lot to the welfare of small farmers worldwide. Its development is limited by severe diseases. In South America, the main fungal disease of rubber trees is the South American leaf blight (SALB) caused by the ascomycete Microcyclus ulei. This fungus inhibits natural rubber production on a commercial scale in South and Central America. Scope The disease is still restricted to its continent of origin, but its potential to be distributed around the world rises with every transcontinental airline connection that directly links tropical regions. The need to develop control measures against the disease is an urgent task and must be carried out on an international scale. All control efforts so far taken since 1910 have ended in a miserable failure. Even the use of modern systemic fungicides and use of greatly improved application techniques have failed to prevent large losses and dieback of trees. The results of research dealing with both the disease and the pathosystem over more than 50 years are summarized and placed into perspective. Future Prospects A detailed knowledge of this host–pathogen combination requires understanding of the dynamics of Hevea leaf development, the biochemical potential for cyanide liberation, and molecular data for several types of resistance factors. Resolution of the Hevea–SALB problem may serve as a model for future host–pathogen studies of perennial plants requiring a holistic approach. PMID:17650512
Development of a database system for mapping insertional mutations onto the mouse genome with large-scale experimental data

PubMed Central

2009-01-01

Background Insertional mutagenesis is an effective method for functional genomic studies in various organisms. It can rapidly generate easily tractable mutations. A large-scale insertional mutagenesis with the piggyBac (PB) transposon is currently performed in mice at the Institute of Developmental Biology and Molecular Medicine (IDM), Fudan University in Shanghai, China. This project is carried out via collaborations among multiple groups overseeing interconnected experimental steps and generates a large volume of experimental data continuously. Therefore, the project calls for an efficient database system for recording, management, statistical analysis, and information exchange. Results This paper presents a database application called MP-PBmice (insertional mutation mapping system of PB Mutagenesis Information Center), which is developed to serve the on-going large-scale PB insertional mutagenesis project. A lightweight enterprise-level development framework Struts-Spring-Hibernate is used here to ensure constructive and flexible support to the application. The MP-PBmice database system has three major features: strict access-control, efficient workflow control, and good expandability. It supports the collaboration among different groups that enter data and exchange information on daily basis, and is capable of providing real time progress reports for the whole project. MP-PBmice can be easily adapted for other large-scale insertional mutation mapping projects and the source code of this software is freely available at http://www.idmshanghai.cn/PBmice. Conclusion MP-PBmice is a web-based application for large-scale insertional mutation mapping onto the mouse genome, implemented with the widely used framework Struts-Spring-Hibernate. This system is already in use by the on-going genome-wide PB insertional mutation mapping project at IDM, Fudan University. PMID:19958505
A reduced basis method for molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Vincent-Finley, Rachel Elisabeth

In this dissertation, we develop a method for molecular simulation based on principal component analysis (PCA) of a molecular dynamics trajectory and least squares approximation of a potential energy function. Molecular dynamics (MD) simulation is a computational tool used to study molecular systems as they evolve through time. With respect to protein dynamics, local motions, such as bond stretching, occur within femtoseconds, while rigid body and large-scale motions, occur within a range of nanoseconds to seconds. To capture motion at all levels, time steps on the order of a femtosecond are employed when solving the equations of motion and simulations must continue long enough to capture the desired large-scale motion. To date, simulations of solvated proteins on the order of nanoseconds have been reported. It is typically the case that simulations of a few nanoseconds do not provide adequate information for the study of large-scale motions. Thus, the development of techniques that allow longer simulation times can advance the study of protein function and dynamics. In this dissertation we use principal component analysis (PCA) to identify the dominant characteristics of an MD trajectory and to represent the coordinates with respect to these characteristics. We augment PCA with an updating scheme based on a reduced representation of a molecule and consider equations of motion with respect to the reduced representation. We apply our method to butane and BPTI and compare the results to standard MD simulations of these molecules. Our results indicate that the molecular activity with respect to our simulation method is analogous to that observed in the standard MD simulation with simulations on the order of picoseconds.
Effects of dynamic heterogeneity and density scaling of molecular dynamics on the relationship among thermodynamic coefficients at the glass transition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koperwas, K., E-mail: kkoperwas@us.edu.pl; Grzybowski, A.; Grzybowska, K.

2015-07-14

In this paper, we define and experimentally verify thermodynamic characteristics of the liquid-glass transition, taking into account a kinetic origin of the process. Using the density scaling law and the four-point measure of the dynamic heterogeneity of molecular dynamics of glass forming liquids, we investigate contributions of enthalpy, temperature, and density fluctuations to spatially heterogeneous molecular dynamics at the liquid-glass transition, finding an equation for the pressure coefficient of the glass transition temperature, dTg/dp. This equation combined with our previous formula for dTg/dp, derived solely from the density scaling criterion, implies a relationship among thermodynamic coefficients at Tg. Since thismore » relationship and both the equations for dTg/dp are very well validated using experimental data at Tg, they are promising alternatives to the classical Prigogine-Defay ratio and both the Ehrenfest equations in case of the liquid-glass transition.« less
Molecular dynamics at low time resolution.

PubMed

Faccioli, P

2010-10-28

The internal dynamics of macromolecular systems is characterized by widely separated time scales, ranging from fraction of picoseconds to nanoseconds. In ordinary molecular dynamics simulations, the elementary time step Δt used to integrate the equation of motion needs to be chosen much smaller of the shortest time scale in order not to cut-off physical effects. We show that in systems obeying the overdamped Langevin equation, it is possible to systematically correct for such discretization errors. This is done by analytically averaging out the fast molecular dynamics which occurs at time scales smaller than Δt, using a renormalization group based technique. Such a procedure gives raise to a time-dependent calculable correction to the diffusion coefficient. The resulting effective Langevin equation describes by construction the same long-time dynamics, but has a lower time resolution power, hence it can be integrated using larger time steps Δt. We illustrate and validate this method by studying the diffusion of a point-particle in a one-dimensional toy model and the denaturation of a protein.
Computational Modeling of Airway and Pulmonary Vascular Structure and Function: Development of a “Lung Physiome”

PubMed Central

Tawhai, M. H.; Clark, A. R.; Donovan, G. M.; Burrowes, K. S.

2011-01-01

Computational models of lung structure and function necessarily span multiple spatial and temporal scales, i.e., dynamic molecular interactions give rise to whole organ function, and the link between these scales cannot be fully understood if only molecular or organ-level function is considered. Here, we review progress in constructing multiscale finite element models of lung structure and function that are aimed at providing a computational framework for bridging the spatial scales from molecular to whole organ. These include structural models of the intact lung, embedded models of the pulmonary airways that couple to model lung tissue, and models of the pulmonary vasculature that account for distinct structural differences at the extra- and intra-acinar levels. Biophysically based functional models for tissue deformation, pulmonary blood flow, and airway bronchoconstriction are also described. The development of these advanced multiscale models has led to a better understanding of complex physiological mechanisms that govern regional lung perfusion and emergent heterogeneity during bronchoconstriction. PMID:22011236

Colored spectrum characteristics of thermal noise on the molecular scale.

PubMed

Zhu, Zhi; Sheng, Nan; Fang, Haiping; Wan, Rongzheng

2016-11-02

Thermal noise is of fundamental importance to many processes. Traditionally, thermal noise has been treated as white noise on the macroscopic scale. Using molecular dynamics simulations and power spectrum analysis, we show that the thermal noise of solute molecules in water is non-white on the molecular scale, which is in contrast to the conventional theory. In the frequency domain from 2 × 10 11 Hz to 10 13 Hz, the power spectrum of thermal noise for polar solute molecules resembles the spectrum of 1/f noise. The power spectrum of thermal noise for non-polar solute molecules deviates only slightly from the spectrum of white noise. The key to this phenomenon is the existence of hydrogen bonds between polar solute molecules and solvent water molecules. Furthermore, for polar solute molecules, the degree of power spectrum deviation from that of white noise is associated with the average lifetime of the hydrogen bonds between the solute and the solvent molecules.
Energy Decomposition Analysis Based on Absolutely Localized Molecular Orbitals for Large-Scale Density Functional Theory Calculations in Drug Design.

PubMed

Phipps, M J S; Fox, T; Tautermann, C S; Skylaris, C-K

2016-07-12

We report the development and implementation of an energy decomposition analysis (EDA) scheme in the ONETEP linear-scaling electronic structure package. Our approach is hybrid as it combines the localized molecular orbital EDA (Su, P.; Li, H. J. Chem. Phys., 2009, 131, 014102) and the absolutely localized molecular orbital EDA (Khaliullin, R. Z.; et al. J. Phys. Chem. A, 2007, 111, 8753-8765) to partition the intermolecular interaction energy into chemically distinct components (electrostatic, exchange, correlation, Pauli repulsion, polarization, and charge transfer). Limitations shared in EDA approaches such as the issue of basis set dependence in polarization and charge transfer are discussed, and a remedy to this problem is proposed that exploits the strictly localized property of the ONETEP orbitals. Our method is validated on a range of complexes with interactions relevant to drug design. We demonstrate the capabilities for large-scale calculations with our approach on complexes of thrombin with an inhibitor comprised of up to 4975 atoms. Given the capability of ONETEP for large-scale calculations, such as on entire proteins, we expect that our EDA scheme can be applied in a large range of biomolecular problems, especially in the context of drug design.
A PORTRAIT OF COLD GAS IN GALAXIES AT 60 pc RESOLUTION AND A SIMPLE METHOD TO TEST HYPOTHESES THAT LINK SMALL-SCALE ISM STRUCTURE TO GALAXY-SCALE PROCESSES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leroy, Adam K.; Hughes, Annie; Schruba, Andreas

2016-11-01

The cloud-scale density, velocity dispersion, and gravitational boundedness of the interstellar medium (ISM) vary within and among galaxies. In turbulent models, these properties play key roles in the ability of gas to form stars. New high-fidelity, high-resolution surveys offer the prospect to measure these quantities across galaxies. We present a simple approach to make such measurements and to test hypotheses that link small-scale gas structure to star formation and galactic environment. Our calculations capture the key physics of the Larson scaling relations, and we show good correspondence between our approach and a traditional “cloud properties” treatment. However, we argue thatmore » our method is preferable in many cases because of its simple, reproducible characterization of all emission. Using, low- J {sup 12}CO data from recent surveys, we characterize the molecular ISM at 60 pc resolution in the Antennae, the Large Magellanic Cloud (LMC), M31, M33, M51, and M74. We report the distributions of surface density, velocity dispersion, and gravitational boundedness at 60 pc scales and show galaxy-to-galaxy and intragalaxy variations in each. The distribution of flux as a function of surface density appears roughly lognormal with a 1 σ width of ∼0.3 dex, though the center of this distribution varies from galaxy to galaxy. The 60 pc resolution line width and molecular gas surface density correlate well, which is a fundamental behavior expected for virialized or free-falling gas. Varying the measurement scale for the LMC and M31, we show that the molecular ISM has higher surface densities, lower line widths, and more self-gravity at smaller scales.« less
Facile transfer of thickness controllable poly(methyl methacrylate) patterns on a nanometer scale onto SiO2 substrates via microcontact printing combined with simplified Langmuir-Schaefer technique.

PubMed

Kim, Yong-Kwan; Kim, Dae-Il; Park, Jaehyun; Shin, Gunchul; Kim, Gyu Tae; Ha, Jeong Sook

2008-12-16

We report on the facile patterning of poly(methyl methacrylate) (PMMA) layers onto SiO2 substrates via microcontact printing combined with the simplified Langmuir-Schaefer (LS) technique. Langmuir film of PMMA was formed just by dropping a dilute PMMA solution onto the air/water surface in a glass Petri dish via self-assembly, and it was used as an ink for the patterned poly(dimethylsilioxane) (PDMS) stamp. The transferred film properties were systematically investigated with variation of postannealing temperature, molecular weight of PMMA, and the inking number. The patterned PMMA film surface was smooth with no vacancy defect in a few micrometers scale AFM images over the whole film area after post-annealing process. The thickness of the PMMA patterns was controlled on the nanometer scale by the number of inkings of the LS layer of PMMA on the PDMS stamp. By using the PMMA patterns as a barrier and a sacrificial layer against the chemical etching and metal deposition, SiO2 and metal patterns were fabricated, respectively. The PMMA layers also worked as a passivation layer against the patterning of V2O5 nanowires and the selective adsorption of single-walled carbon nanotubes (SWCNTs). We also fabricated thin film transistors using patterned SWCNTs with different percolation states and investigated the electrical properties.
The temperature of large dust grains in molecular clouds

NASA Technical Reports Server (NTRS)

Clark, F. O.; Laureijs, R. J.; Prusti, T.

1991-01-01

The temperature of the large dust grains is calculated from three molecular clouds ranging in visual extinction from 2.5 to 8 mag, by comparing maps of either extinction derived from star counts or gas column density derived from molecular observations to I(100). Both techniques show the dust temperature declining into clouds. The two techniques do not agree in absolute scale.
Gait and Functional Mobility Deficits in Fragile X-Associated Tremor/Ataxia Syndrome.

PubMed

O'Keefe, Joan A; Robertson-Dick, Erin E; Hall, Deborah A; Berry-Kravis, Elizabeth

2016-08-01

Fragile X-associated tremor/ataxia syndrome (FXTAS) results from a "premutation" (PM) size CGG repeat expansion in the fragile X mental retardation 1 (FMR1) gene. Cerebellar gait ataxia is the primary feature in some FXTAS patients causing progressive disability. However, no studies have quantitatively characterized gait and mobility deficits in FXTAS. We performed quantitative gait and mobility analysis in seven FMR1 PM carriers with FXTAS and ataxia, six PM carriers without FXTAS, and 18 age-matched controls. We studied four independent gait domains, trunk range of motion (ROM), and movement transitions using an instrumented Timed Up and Go (i-TUG). We correlated these outcome measures with FMR1 molecular variables and clinical severity scales. PM carriers with FXTAS were globally impaired in every gait performance domain except trunk ROM compared to controls. These included total i-TUG duration, stride velocity, gait cycle time, cadence, double-limb support and swing phase times, turn duration, step time before turn, and turn-to-sit duration, and increased gait variability on several measures. Carriers without FXTAS did not differ from controls on any parameters, but double-limb support time was close to significance. Balance and disability scales correlated with multiple gait and movement transition parameters, while the FXTAS Rating Scale did not. This is the first study to quantitatively examine gait and movement transitions in FXTAS patients. Gait characteristics were consistent with those from previous cohorts with cerebellar ataxia. Sensitive measures like the i-TUG may help determine efficacy of interventions, characterize disease progression, and provide early markers of disease in FXTAS.
Vanishing-Overhead Linear-Scaling Random Phase Approximation by Cholesky Decomposition and an Attenuated Coulomb-Metric.

PubMed

Luenser, Arne; Schurkus, Henry F; Ochsenfeld, Christian

2017-04-11

A reformulation of the random phase approximation within the resolution-of-the-identity (RI) scheme is presented, that is competitive to canonical molecular orbital RI-RPA already for small- to medium-sized molecules. For electronically sparse systems drastic speedups due to the reduced scaling behavior compared to the molecular orbital formulation are demonstrated. Our reformulation is based on two ideas, which are independently useful: First, a Cholesky decomposition of density matrices that reduces the scaling with basis set size for a fixed-size molecule by one order, leading to massive performance improvements. Second, replacement of the overlap RI metric used in the original AO-RPA by an attenuated Coulomb metric. Accuracy is significantly improved compared to the overlap metric, while locality and sparsity of the integrals are retained, as is the effective linear scaling behavior.
Materials-by-design: computation, synthesis, and characterization from atoms to structures

NASA Astrophysics Data System (ADS)

Yeo, Jingjie; Jung, Gang Seob; Martín-Martínez, Francisco J.; Ling, Shengjie; Gu, Grace X.; Qin, Zhao; Buehler, Markus J.

2018-05-01

In the 50 years that succeeded Richard Feynman’s exposition of the idea that there is ‘plenty of room at the bottom’ for manipulating individual atoms for the synthesis and manufacturing processing of materials, the materials-by-design paradigm is being developed gradually through synergistic integration of experimental material synthesis and characterization with predictive computational modeling and optimization. This paper reviews how this paradigm creates the possibility to develop materials according to specific, rational designs from the molecular to the macroscopic scale. We discuss promising techniques in experimental small-scale material synthesis and large-scale fabrication methods to manipulate atomistic or macroscale structures, which can be designed by computational modeling. These include recombinant protein technology to produce peptides and proteins with tailored sequences encoded by recombinant DNA, self-assembly processes induced by conformational transition of proteins, additive manufacturing for designing complex structures, and qualitative and quantitative characterization of materials at different length scales. We describe important material characterization techniques using numerous methods of spectroscopy and microscopy. We detail numerous multi-scale computational modeling techniques that complements these experimental techniques: DFT at the atomistic scale; fully atomistic and coarse-grain molecular dynamics at the molecular to mesoscale; continuum modeling at the macroscale. Additionally, we present case studies that utilize experimental and computational approaches in an integrated manner to broaden our understanding of the properties of two-dimensional materials and materials based on silk and silk-elastin-like proteins.
Influence of galactic arm scale dynamics on the molecular composition of the cold and dense ISM. I. Observed abundance gradients in dense clouds

NASA Astrophysics Data System (ADS)

Ruaud, M.; Wakelam, V.; Gratier, P.; Bonnell, I. A.

2018-04-01

Aim. We study the effect of large scale dynamics on the molecular composition of the dense interstellar medium during the transition between diffuse to dense clouds. Methods: We followed the formation of dense clouds (on sub-parsec scales) through the dynamics of the interstellar medium at galactic scales. We used results from smoothed particle hydrodynamics (SPH) simulations from which we extracted physical parameters that are used as inputs for our full gas-grain chemical model. In these simulations, the evolution of the interstellar matter is followed for 50 Myr. The warm low-density interstellar medium gas flows into spiral arms where orbit crowding produces the shock formation of dense clouds, which are held together temporarily by the external pressure. Results: We show that depending on the physical history of each SPH particle, the molecular composition of the modeled dense clouds presents a high dispersion in the computed abundances even if the local physical properties are similar. We find that carbon chains are the most affected species and show that these differences are directly connected to differences in (1) the electronic fraction, (2) the C/O ratio, and (3) the local physical conditions. We argue that differences in the dynamical evolution of the gas that formed dense clouds could account for the molecular diversity observed between and within these clouds. Conclusions: This study shows the importance of past physical conditions in establishing the chemical composition of the dense medium.
Scalable Molecular Dynamics with NAMD

PubMed Central

Phillips, James C.; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D.; Kalé, Laxmikant; Schulten, Klaus

2008-01-01

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This paper, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Next, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, e.g., the Tcl scripting language. Finally, the paper provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. PMID:16222654
Release of aged contaminants from weathered sediments: Effects of sorbate speciation on scaling of reactive transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chorover, Jon; Perdrial, Nico; Mueller, Karl

2012-11-05

Hanford sediments impacted by hyperalkaline high level radioactive waste have undergone incongruent silicate mineral weathering concurrent with contaminant uptake. In this project, we studied the impact of background pore water (BPW) on strontium, cesium and iodine desorption and transport in Hanford sediments that were experimentally weathered by contact with simulated hyperalkaline tank waste leachate (STWL) solutions. Using those lab-weathered Hanford sediments (HS) and model precipitates formed during nucleation from homogeneous STWL solutions (HN), we (i) provided thorough characterization of reaction products over a matrix of field-relevant gradients in contaminant concentration, partial pressure of carbon dioxide, and reaction time; (ii) improvedmore » molecular-scale understanding of how sorbate speciation controls contaminant desorption from weathered sediments upon removal of caustic sources; and (iii) developed a mechanistic, predictive model of meso- to field-scale contaminant reactive transport under these conditions. In this final report, we provide detailed descriptions of our results from this three-year study, completed in 2012 following a one-year no cost extension.« less
Release of Aged Contaminants from weathered sediments: Effects of sorbate speciation on scaling of reactive transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chorover, Jon; Perdrial, Nico; Mueller, Karl

2012-08-14

Hanford sediments impacted by hyperalkaline high level radioactive waste have undergone incongruent silicate mineral weathering concurrent with contaminant uptake (Chorover et al., 2008). In this project, we studied the impact of background pore water (BPW) on strontium, cesium and iodine desorption and transport in Hanford sediments that were experimentally weathered by contact with simulated hyperalkaline tank waste leachate (STWL) solutions. Using those lab-weathered Hanford sediments (HS) and model precipitates formed during nucleation from homogeneous STWL solutions (HN), we (i) provided thorough characterization of reaction products over a matrix of field-relevant gradients in contaminant concentration, P CO2, and reaction time; (ii)more » improved molecular-scale understanding of how sorbate speciation controls contaminant desorption from weathered sediments upon removal of caustic sources; and (iii) developed a mechanistic, predictive model of meso- to field-scale contaminant reactive transport under these conditions. Below, we provide some detailed descriptions of our results from this three year study, recently completed following a one-year no cost extension.« less
Modeling systems-level dynamics: Understanding without mechanistic explanation in integrative systems biology.

PubMed

MacLeod, Miles; Nersessian, Nancy J

2015-02-01

In this paper we draw upon rich ethnographic data of two systems biology labs to explore the roles of explanation and understanding in large-scale systems modeling. We illustrate practices that depart from the goal of dynamic mechanistic explanation for the sake of more limited modeling goals. These processes use abstract mathematical formulations of bio-molecular interactions and data fitting techniques which we call top-down abstraction to trade away accurate mechanistic accounts of large-scale systems for specific information about aspects of those systems. We characterize these practices as pragmatic responses to the constraints many modelers of large-scale systems face, which in turn generate more limited pragmatic non-mechanistic forms of understanding of systems. These forms aim at knowledge of how to predict system responses in order to manipulate and control some aspects of them. We propose that this analysis of understanding provides a way to interpret what many systems biologists are aiming for in practice when they talk about the objective of a "systems-level understanding." Copyright © 2014 Elsevier Ltd. All rights reserved.
Nitrate promotes biological oxidation of sulfide in wastewaters: experiment at plant-scale.

PubMed

García de Lomas, Juan; Corzo, Alfonso; Gonzalez, Juan M; Andrades, Jose A; Iglesias, Emilio; Montero, María José

2006-03-05

Biogenic production of sulfide in wastewater treatment plants involves odors, toxicity and corrosion problems. The production of sulfide is a consequence of bacterial activity, mainly sulfate-reducing bacteria (SRB). To prevent this production, the efficiency of nitrate addition to wastewater was tested at plant-scale by dosing concentrated calcium nitrate (Nutriox) in the works inlet. Nutriox dosing resulted in a sharp decrease of sulfide, both in the air and in the bulk water, reaching maximum decreases of 98.7% and 94.7%, respectively. Quantitative molecular microbiology techniques indicated that the involved mechanism is the development of the nitrate-reducing, sulfide-oxidizing bacterium Thiomicrospira denitrificans instead of the direct inhibition of the SRB community. Denitrification rate in primary sedimentation tanks was enhanced by nitrate, being this almost completely consumed. No significant increase of inorganic nitrogen was found in the discharged effluent, thus reducing potential environmental hazards to receiving waters. This study demonstrates the effectiveness of nitrate addition in controlling sulfide generation at plant-scale, provides the mechanism and supports the environmental adequacy of this strategy.
Differential Response to Heat Stress in Outer and Inner Onion Bulb Scales.

PubMed

Galsurker, Ortal; Doron-Faigenboim, Adi; Teper-Bamnolker, Paula; Daus, Avinoam; Lers, Amnon; Eshel, Dani

2018-05-18

Brown protective skin formation in onion bulbs can be induced by rapid postharvest heat treatment. Onions that were peeled to different depths and were exposed to heat stress showed that only the outer scale formed dry brown skin, whereas the inner scales maintained high water content and did not change color. Our results reveal that browning of the outer scale during heat treatment is due to an enzymatic process that is associated with high levels of oxidation components, such as peroxidase and quercetin glucoside. De-novo transcriptome analysis revealed differential molecular responses of the outer and inner scales to the heat stress. Genes involved in lipid metabolism, oxidation pathways and cell-wall modification were highly expressed in the outer scale during heating. Defense-response-related genes such as those encoding heat-shock proteins, antioxidative stress defense or production of osmoprotectant metabolites were mostly induced in the inner scale in response to the heat exposure. These transcriptomic data led to a conceptual model that suggests sequential processes for browning development and desiccation of the outer scales versus processes associated with defense response and heat tolerance in the inner scale. Thus, the observed physiological differences between the outer and inner scales is supported by the identified molecular differences.
Universal scaling in the aging of the strong glass former SiO{sub 2}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vollmayr-Lee, Katharina, E-mail: kvollmay@bucknell.edu; Gorman, Christopher H.; Castillo, Horacio E.

We show that the aging dynamics of a strong glass former displays a strikingly simple scaling behavior, connecting the average dynamics with its fluctuations, namely, the dynamical heterogeneities. We perform molecular dynamics simulations of SiO{sub 2} with van Beest-Kramer-van Santen interactions, quenching the system from high to low temperature, and study the evolution of the system as a function of the waiting time t{sub w} measured from the instant of the quench. We find that both the aging behavior of the dynamic susceptibility χ{sub 4} and the aging behavior of the probability distribution P(f{sub s,r}) of the local incoherent intermediatemore » scattering function f{sub s,r} can be described by simple scaling forms in terms of the global incoherent intermediate scattering function C. The scaling forms are the same that have been found to describe the aging of several fragile glass formers and that, in the case of P(f{sub s,r}), have been also predicted theoretically. A thorough study of the length scales involved highlights the importance of intermediate length scales. We also analyze directly the scaling dependence on particle type and on wavevector q and find that both the average and the fluctuations of the slow aging dynamics are controlled by a unique aging clock, which is not only independent of the wavevector q, but is also the same for O and Si atoms.« less
Biologically-Mediated Weathering of Minerals From Nanometre Scale to Environmental Systems

NASA Astrophysics Data System (ADS)

Brown, D. J.; Banwart, S. A.; Smits, M. M.; Leake, J. R.; Bonneville, S.; Benning, L. G.; Haward, S. J.; Ragnarsdottir, K.

2007-12-01

The Weathering Science Consortium is a multi-disciplinary project that aims to create a step change in understanding how biota control mineral weathering and soil formation (http://www.wun.ac.uk/wsc). Our hypothesis is that rates of biotic weathering are driven by the energy supply from plants to the organisms, controlling their biomass, surface area of contact with minerals and their capacity to interact chemically with minerals. Symbiotic fungal mycorrhiza of 90% of plant species are empowered with an available carbohydrate supply from plants that is unparalleled amongst soil microbes. They develop extensive mycelial networks that intimately contact minerals, which they weather aggressively. We hypothesise that mycorrhiza play a critical role through their focussing of photosynthate energy from plants into sub-surface weathering environments. Our work identifies how these fungal cells, and their secretions, interact with mineral surfaces and affect the rates of nutrient transfer from minerals to the organism. Investigating these living systems allows us to create new concepts and mathematical models that can describe biological weathering and be used in computer simulations of soil weathering dynamics. We are studying these biochemical interactions at 3 levels of observation: 1. At the molecular scale to understand interactions between living cells and minerals and to quantify the chemistry that breaks down the mineral structure; 2. At the soil grain scale to quantify the activity and spatial distribution of the fungi, roots and other organisms (e.g. bacteria) and their effects on the rates at which minerals are dissolved to release nutrients; 3. At soil profile scale to test models for the spatial distribution of active fungi and carbon energy and their seasonal variability and impact on mineral dissolution rates. Here we present early results from molecular and soil grain scale experiments. We have grown pure culture (Suillus bovinus, Paxillus involutus) mycorrhizal mycelial networks associated with pine trees in otherwise sterile (agar) and also non-sterile (peat) microcosms, which include mineral sections and powders of biotite, apatite and quartz. 14C labelling has been used to map C flux through the microcosms and to determine the transfer of photosynthate energy into the weathering arenas. We have used Vertical Scanning Interferometry (VSI) to assess volumetric alteration of mineral substrates in contact with fungi. Focused Ion Beam (FIB)- Transmission Electron Microscope (TEM) work provides evidence for increased mechanical forcing and possible alteration of biotite surfaces with greater fungi contact time. We also present real-time in situ observations of mineral-organic acid and mineral-exudate interactions using Atomic Force Microscopy (AFM).
Molecular dynamics simulations of graphoepitaxy of organic semiconductors, sexithiophene, and pentacene: Molecular-scale mechanisms of organic graphoepitaxy

NASA Astrophysics Data System (ADS)

Ikeda, Susumu

2018-03-01

Molecular dynamics (MD) simulations of the organic semiconductors α-sexithiophene (6T) and pentacene were carried out to clarify the mechanism of organic graphoepitaxy at the molecular level. First, the models of the grooved substrates were made and the surfaces of the inside of the grooves were modified with -OH or -OSi(CH3)3, making the surfaces hydrophilic or hydrophobic. By the MD simulations of 6T, it was found that three stable azimuthal directions exist (0, ˜45, and 90° the angle that the c-axis makes with the groove), being consistent with experimental results. MD simulations of deposition processes of 6T and pentacene were also carried out, and pentacene molecules showed the spontaneous formation of herringbone packing during deposition. Some pentacene molecules stood on the surface and formed a cluster whose a-axis was parallel to the groove. It is expected that a deep understanding of the molecular-scale mechanisms will lead graphoepitaxy to practical applications, improving the performance of organic devices.
Quantitative Reactivity Scales for Dynamic Covalent and Systems Chemistry.

PubMed

Zhou, Yuntao; Li, Lijie; Ye, Hebo; Zhang, Ling; You, Lei

2016-01-13

Dynamic covalent chemistry (DCC) has become a powerful tool for the creation of molecular assemblies and complex systems in chemistry and materials science. Herein we developed for the first time quantitative reactivity scales capable of correlation and prediction of the equilibrium of dynamic covalent reactions (DCRs). The reference reactions are based upon universal DCRs between imines, one of the most utilized structural motifs in DCC, and a series of O-, N-, and S- mononucleophiles. Aromatic imines derived from pyridine-2-carboxyaldehyde exhibit capability for controlling the equilibrium through distinct substituent effects. Electron-donating groups (EDGs) stabilize the imine through quinoidal resonance, while electron-withdrawing groups (EWGs) stabilize the adduct by enhancing intramolecular hydrogen bonding, resulting in curvature in Hammett analysis. Notably, unique nonlinearity induced by both EDGs and EWGs emerged in Hammett plot when cyclic secondary amines were used. This is the first time such a behavior is observed in a thermodynamically controlled system, to the best of our knowledge. Unified quantitative reactivity scales were proposed for DCC and defined by the correlation log K = S(N) (R(N) + R(E)). Nucleophilicity parameters (R(N) and S(N)) and electrophilicity parameters (R(E)) were then developed from DCRs discovered. Furthermore, the predictive power of those parameters was verified by successful correlation of other DCRs, validating our reactivity scales as a general and useful tool for the evaluation and modeling of DCRs. The reactivity parameters proposed here should be complementary to well-established kinetics based parameters and find applications in many aspects, such as DCR discovery, bioconjugation, and catalysis.
Predictive Mechanical Characterization of Macro-Molecular Material Chemistry Structures of Cement Paste at Nano Scale - Two-phase Macro-Molecular Structures of Calcium Silicate Hydrate, Tri-Calcium Silicate, Di-Calcium Silicate and Calcium Hydroxide

NASA Astrophysics Data System (ADS)

Padilla Espinosa, Ingrid Marcela

Concrete is a hierarchical composite material with a random structure over a wide range of length scales. At submicron length scale the main component of concrete is cement paste, formed by the reaction of Portland cement clinkers and water. Cement paste acts as a binding matrix for the other components and is responsible for the strength of concrete. Cement paste microstructure contains voids, hydrated and unhydrated cement phases. The main crystalline phases of unhydrated cement are tri-calcium silicate (C3S) and di-calcium silicate (C2S), and of hydrated cement are calcium silicate hydrate (CSH) and calcium hydroxide (CH). Although efforts have been made to comprehend the chemical and physical nature of cement paste, studies at molecular level have primarily been focused on individual components. Present research focuses on the development of a method to model, at molecular level, and analysis of the two-phase combination of hydrated and unhydrated phases of cement paste as macromolecular systems. Computational molecular modeling could help in understanding the influence of the phase interactions on the material properties, and mechanical performance of cement paste. Present work also strives to create a framework for molecular level models suitable for potential better comparisons with low length scale experimental methods, in which the sizes of the samples involve the mixture of different hydrated and unhydrated crystalline phases of cement paste. Two approaches based on two-phase cement paste macromolecular structures, one involving admixed molecular phases, and the second involving cluster of two molecular phases are investigated. The mechanical properties of two-phase macromolecular systems of cement paste consisting of key hydrated phase CSH and unhydrated phases C3S or C2S, as well as CSH with the second hydrated phase CH were calculated. It was found that these cement paste two-phase macromolecular systems predicted an isotropic material behavior. Also, these systems exhibited a high bulk modulus, compared to the elastic modulus. These results are an indication and concur with the high compression strength of cement paste seen at engineering length scale. In addition, the bulk modulus of two-phase systems consisting of hydrated CSH and unhydrated C3S or C2S was found to increase with higher levels of unhydrated components. The interaction energies of two-phase cement paste molecular structures studied in the present work were calculated, showing that a higher interaction is attained when the two phases are admixed as small components instead of cluster of phases. Finally, the mechanical behavior under shear deformation was predicted by using a quasi-static deformation method and analyzed for a representative two-phase (CSH and C2S) macromolecular structure of cement paste.

Some links on this page may take you to non-federal websites. Their policies may differ from this site.