High-Resolution “Fleezers”: Dual-Trap Optical Tweezers Combined with Single-Molecule Fluorescence Detection

PubMed Central

Whitley, Kevin D.; Comstock, Matthew J.; Chemla, Yann R.

2017-01-01

Recent advances in optical tweezers have greatly expanded their measurement capabilities. A new generation of hybrid instrument that combines nanomechanical manipulation with fluorescence detection—fluorescence optical tweezers, or “fleezers”—is providing a powerful approach to study complex macromolecular dynamics. Here, we describe a combined high-resolution optical trap/confocal fluorescence microscope that can simultaneously detect sub-nanometer displacements, sub-piconewton forces, and single-molecule fluorescence signals. The primary technical challenge to these hybrid instruments is how to combine both measurement modalities without sacrificing the sensitivity of either one. We present general design principles to overcome this challenge and provide detailed, step-by-step instructions to implement them in the construction and alignment of the instrument. Lastly, we present a set of protocols to perform a simple, proof-of-principle experiment that highlights the instrument capabilities. PMID:27844430

Optoelectrical Cooling of Formaldehyde to Sub-Millikelvin Temperatures

NASA Astrophysics Data System (ADS)

Zeppenfeld, Martin

2016-05-01

Due to their strong long-range dipole-dipole interactions and large number of internal states, polar molecules cooled to ultracold temperatures enable fascinating applications ranging from ultracold chemistry to investigation of dipolar quantum gases. However, realizing a simple and general technique to cool molecules to ultracold temperatures, akin to laser cooling of atoms, has been a formidable challenge. We present results for opto-electrical Sisyphus cooling applied to formaldehyde (H2 CO). In this generally applicable cooling scheme, molecules repeatedly move up and down electric field gradients of a trapping potential in different rotational states to efficiently extract kinetic energy. A total of about 300,000 molecules are thereby cooled by a factor of 1000 to 400uK, resulting in a record-large ensemble of ultracold molecules. In addition to cooling of the motional degrees of freedom, optical pumping via a vibrational transition allows us to control the internal rotational state. We thereby achieve a purity of over 80% of formaldehyde molecules in a single rotational M-sublevel. Our experiment provides an excellent starting point for precision spectroscopy and investigation of ultracold collisions.

Covariance Matrix Estimation for the Cryo-EM Heterogeneity Problem*

PubMed Central

Katsevich, E.; Katsevich, A.; Singer, A.

2015-01-01

In cryo-electron microscopy (cryo-EM), a microscope generates a top view of a sample of randomly oriented copies of a molecule. The problem of single particle reconstruction (SPR) from cryo-EM is to use the resulting set of noisy two-dimensional projection images taken at unknown directions to reconstruct the three-dimensional (3D) structure of the molecule. In some situations, the molecule under examination exhibits structural variability, which poses a fundamental challenge in SPR. The heterogeneity problem is the task of mapping the space of conformational states of a molecule. It has been previously suggested that the leading eigenvectors of the covariance matrix of the 3D molecules can be used to solve the heterogeneity problem. Estimating the covariance matrix is challenging, since only projections of the molecules are observed, but not the molecules themselves. In this paper, we formulate a general problem of covariance estimation from noisy projections of samples. This problem has intimate connections with matrix completion problems and high-dimensional principal component analysis. We propose an estimator and prove its consistency. When there are finitely many heterogeneity classes, the spectrum of the estimated covariance matrix reveals the number of classes. The estimator can be found as the solution to a certain linear system. In the cryo-EM case, the linear operator to be inverted, which we term the projection covariance transform, is an important object in covariance estimation for tomographic problems involving structural variation. Inverting it involves applying a filter akin to the ramp filter in tomography. We design a basis in which this linear operator is sparse and thus can be tractably inverted despite its large size. We demonstrate via numerical experiments on synthetic datasets the robustness of our algorithm to high levels of noise. PMID:25699132

A challenge for green chemistry: designing molecules that readily dissolve in carbon dioxide.

PubMed

Beckman, E J

2004-09-07

Carbon dioxide is a green yet feeble solvent whose full potential won't be realized until we develop a more thorough understanding of its solvent behavior at the molecular level. Fortunately, advances in molecular modeling coupled with experiments are rapidly improving our understanding of CO(2)'s behavior, permitting design of new, more sustainable "CO(2)-philes".

A novel small molecule mediate 18F-FDG excited fluorescence molecular imaging

NASA Astrophysics Data System (ADS)

Zhang, Zeyu; Guo, Hongbo; Hu, Zhenhua; Tian, Jie

2018-02-01

Fluorescence molecular imaging (FMI) has been widely used in many medical fields with small molecule indocyanine green (ICG). However, low signal-background ratio and limited specificity to tumor remain big challenges for FMI. In this study, a novel excitation strategy is proposed on the basis of clinical approved ICG and 18F-FDG. A series of in vitro experiments are designed to reveal the mechanism and results show obvious decreasing of ICG fluorescence intensity with the increasing distance to excitation source. Meanwhile, the ICG fluorescence intensity is proportional to the activity of radiopharmaceutical. Results from different respects illustrate the promising of this proposed excitation strategy.

Bottom-up construction of artificial molecules for superconducting quantum processors

NASA Astrophysics Data System (ADS)

Poletto, Stefano; Rigetti, Chad; Gambetta, Jay M.; Merkel, Seth; Chow, Jerry M.; Corcoles, Antonio D.; Smolin, John A.; Rozen, Jim R.; Keefe, George A.; Rothwell, Mary B.; Ketchen, Mark B.; Steffen, Matthias

2012-02-01

Recent experiments on transmon qubits capacitively coupled to superconducting 3-dimensional cavities have shown coherence times much longer than transmons coupled to more traditional planar resonators. For the implementation of a quantum processor this approach has clear advantages over traditional techniques but it poses the challenge of scalability. We are currently implementing multi-qubits experiments based on a bottom-up scaling approach. First, transmon qubits are fabricated on individual chips and are independently characterized. Second, an artificial molecule is assembled by selecting a particular set of previously characterized single-transmon chips. We present recent data on a two-qubit artificial molecule constructed in this way. The two qubits are chosen to generate a strong Z-Z interaction by matching the 0-1 transition energy of one qubit with the 1-2 transition of the other. Single qubit manipulations and state tomography cannot be done with ``traditional'' single tone microwave pulses but instead specifically shaped pulses have to be simultaneously applied on both qubits. Coherence times, coupling strength, and optimal pulses for decoupling the two qubits and perform state tomography are presented

MALDI matrices for low molecular weight compounds: an endless story?

PubMed

Calvano, Cosima Damiana; Monopoli, Antonio; Cataldi, Tommaso R I; Palmisano, Francesco

2018-04-23

Since its introduction in the 1980s, matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has gained a prominent role in the analysis of high molecular weight biomolecules such as proteins, peptides, oligonucleotides, and polysaccharides. Its application to low molecular weight compounds has remained for long time challenging due to the spectral interferences produced by conventional organic matrices in the low m/z window. To overcome this problem, specific sample preparation such as analyte/matrix derivatization, addition of dopants, or sophisticated deposition technique especially useful for imaging experiments, have been proposed. Alternative approaches based on second generation (rationally designed) organic matrices, ionic liquids, and inorganic matrices, including metallic nanoparticles, have been the object of intense and continuous research efforts. Definite evidences are now provided that MALDI MS represents a powerful and invaluable analytical tool also for small molecules, including their quantification, thus opening new, exciting applications in metabolomics and imaging mass spectrometry. This review is intended to offer a concise critical overview of the most recent achievements about MALDI matrices capable of specifically address the challenging issue of small molecules analysis. Graphical abstract An ideal Book of matrices for MALDI MS of small molecules.

Spectral properties from Matsubara Green's function approach: Application to molecules

NASA Astrophysics Data System (ADS)

Schüler, M.; Pavlyukh, Y.

2018-03-01

We present results for many-body perturbation theory for the one-body Green's function at finite temperatures using the Matsubara formalism. Our method relies on the accurate representation of the single-particle states in standard Gaussian basis sets, allowing to efficiently compute, among other observables, quasiparticle energies and Dyson orbitals of atoms and molecules. In particular, we challenge the second-order treatment of the Coulomb interaction by benchmarking its accuracy for a well-established test set of small molecules, which includes also systems where the usual Hartree-Fock treatment encounters difficulties. We discuss different schemes how to extract quasiparticle properties and assess their range of applicability. With an accurate solution and compact representation, our method is an ideal starting point to study electron dynamics in time-resolved experiments by the propagation of the Kadanoff-Baym equations.

Small Molecule Injection into Single-Cell C. elegans Embryos via Carbon-Reinforced Nanopipettes

PubMed Central

Morton, Diane G.; Fellman, Shanna M.; Chung, SueYeon; Soltani, Mohammad; Kevek, Joshua W.; McEuen, Paul M.; Kemphues, Kenneth J.; Wang, Michelle D.

2013-01-01

The introduction of chemical inhibitors into living cells at specific times in development is a useful method for investigating the roles of specific proteins or cytoskeletal components in developmental processes. Some embryos, such as those of Caenorhabditis elegans, however, possess a tough eggshell that makes introducing drugs and other molecules into embryonic cells challenging. We have developed a procedure using carbon-reinforced nanopipettes (CRNPs) to deliver molecules into C. elegans embryos with high temporal control. The use of CRNPs allows for cellular manipulation to occur just subsequent to meiosis II with minimal damage to the embryo. We have used our technique to replicate classical experiments using latrunculin A to inhibit microfilaments and assess its effects on early polarity establishment. Our injections of latrunculin A confirm the necessity of microfilaments in establishing anterior-posterior polarity at this early stage, even when microtubules remain intact. Further, we find that latrunculin A treatment does not prevent association of PAR-2 or PAR-6 with the cell cortex. Our experiments demonstrate the application of carbon-reinforced nanopipettes to the study of one temporally-confined developmental event. The use of CRNPs to introduce molecules into the embryo should be applicable to investigations at later developmental stages as well as other cells with tough outer coverings. PMID:24086620

Small molecule injection into single-cell C. elegans embryos via carbon-reinforced nanopipettes.

PubMed

Brennan, Lucy D; Roland, Thibault; Morton, Diane G; Fellman, Shanna M; Chung, SueYeon; Soltani, Mohammad; Kevek, Joshua W; McEuen, Paul M; Kemphues, Kenneth J; Wang, Michelle D

2013-01-01

The introduction of chemical inhibitors into living cells at specific times in development is a useful method for investigating the roles of specific proteins or cytoskeletal components in developmental processes. Some embryos, such as those of Caenorhabditis elegans, however, possess a tough eggshell that makes introducing drugs and other molecules into embryonic cells challenging. We have developed a procedure using carbon-reinforced nanopipettes (CRNPs) to deliver molecules into C. elegans embryos with high temporal control. The use of CRNPs allows for cellular manipulation to occur just subsequent to meiosis II with minimal damage to the embryo. We have used our technique to replicate classical experiments using latrunculin A to inhibit microfilaments and assess its effects on early polarity establishment. Our injections of latrunculin A confirm the necessity of microfilaments in establishing anterior-posterior polarity at this early stage, even when microtubules remain intact. Further, we find that latrunculin A treatment does not prevent association of PAR-2 or PAR-6 with the cell cortex. Our experiments demonstrate the application of carbon-reinforced nanopipettes to the study of one temporally-confined developmental event. The use of CRNPs to introduce molecules into the embryo should be applicable to investigations at later developmental stages as well as other cells with tough outer coverings.

Nuclear magnetic resonance of laser-polarized noble gases in molecules, materials and organisms

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

Goodson, Boyd McLean

1999-12-01

Conventional nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) are fundamentally challenged by the insensitivity that stems from the ordinarily low spin polarization achievable in even the strongest NMR magnets. However, by transferring angular momentum from laser light to electronic and nuclear spins, optical pumping methods can increase the nuclear spin polarization of noble gases by several orders of magnitude, thereby greatly enhancing their NMR sensitivity. This dissertation is primarily concerned with the principles and practice of optically pumped nuclear magnetic resonance (OPNMR). The enormous sensitivity enhancement afforded by optical pumping noble gases can be exploited to permitmore » a variety of novel NMR experiments across many disciplines. Many such experiments are reviewed, including the void-space imaging of organisms and materials, NMR and MRI of living tissues, probing structure and dynamics of molecules in solution and on surfaces, and zero-field NMR and MRI.« less

An ontology for major histocompatibility restriction.

PubMed

Vita, Randi; Overton, James A; Seymour, Emily; Sidney, John; Kaufman, Jim; Tallmadge, Rebecca L; Ellis, Shirley; Hammond, John; Butcher, Geoff W; Sette, Alessandro; Peters, Bjoern

2016-01-01

MHC molecules are a highly diverse family of proteins that play a key role in cellular immune recognition. Over time, different techniques and terminologies have been developed to identify the specific type(s) of MHC molecule involved in a specific immune recognition context. No consistent nomenclature exists across different vertebrate species. To correctly represent MHC related data in The Immune Epitope Database (IEDB), we built upon a previously established MHC ontology and created an ontology to represent MHC molecules as they relate to immunological experiments. This ontology models MHC protein chains from 16 species, deals with different approaches used to identify MHC, such as direct sequencing verses serotyping, relates engineered MHC molecules to naturally occurring ones, connects genetic loci, alleles, protein chains and multi-chain proteins, and establishes evidence codes for MHC restriction. Where available, this work is based on existing ontologies from the OBO foundry. Overall, representing MHC molecules provides a challenging and practically important test case for ontology building, and could serve as an example of how to integrate other ontology building efforts into web resources.

Predicting supramolecular self-assembly on reconstructed metal surfaces

NASA Astrophysics Data System (ADS)

Roussel, Thomas J.; Barrena, Esther; Ocal, Carmen; Faraudo, Jordi

2014-06-01

The prediction of supramolecular self-assembly onto solid surfaces is still challenging in many situations of interest for nanoscience. In particular, no previous simulation approach has been capable to simulate large self-assembly patterns of organic molecules over reconstructed surfaces (which have periodicities over large distances) due to the large number of surface atoms and adsorbing molecules involved. Using a novel simulation technique, we report here large scale simulations of the self-assembly patterns of an organic molecule (DIP) over different reconstructions of the Au(111) surface. We show that on particular reconstructions, the molecule-molecule interactions are enhanced in a way that long-range order is promoted. Also, the presence of a distortion in a reconstructed surface pattern not only induces the presence of long-range order but also is able to drive the organization of DIP into two coexisting homochiral domains, in quantitative agreement with STM experiments. On the other hand, only short range order is obtained in other reconstructions of the Au(111) surface. The simulation strategy opens interesting perspectives to tune the supramolecular structure by simulation design and surface engineering if choosing the right molecular building blocks and stabilising the chosen reconstruction pattern.The prediction of supramolecular self-assembly onto solid surfaces is still challenging in many situations of interest for nanoscience. In particular, no previous simulation approach has been capable to simulate large self-assembly patterns of organic molecules over reconstructed surfaces (which have periodicities over large distances) due to the large number of surface atoms and adsorbing molecules involved. Using a novel simulation technique, we report here large scale simulations of the self-assembly patterns of an organic molecule (DIP) over different reconstructions of the Au(111) surface. We show that on particular reconstructions, the molecule-molecule interactions are enhanced in a way that long-range order is promoted. Also, the presence of a distortion in a reconstructed surface pattern not only induces the presence of long-range order but also is able to drive the organization of DIP into two coexisting homochiral domains, in quantitative agreement with STM experiments. On the other hand, only short range order is obtained in other reconstructions of the Au(111) surface. The simulation strategy opens interesting perspectives to tune the supramolecular structure by simulation design and surface engineering if choosing the right molecular building blocks and stabilising the chosen reconstruction pattern. GA image adapted from refs: (a) Phys. Chem. Chem. Phys., 2001, 3, 3399-3404, with permission from the PCCP Owner Societies, and (b) J. Phys. Chem. C, 2008, 112 (18), 7168-7172, reprinted with permission from the American Chemical Society, copyright © 2008.

Generalization of dielectric-dependent hybrid functionals to finite systems

DOE PAGES

Brawand, Nicholas P.; Voros, Marton; Govoni, Marco; ...

2016-10-04

The accurate prediction of electronic and optical properties of molecules and solids is a persistent challenge for methods based on density functional theory. We propose a generalization of dielectric-dependent hybrid functionals to finite systems where the definition of the mixing fraction of exact and semilocal exchange is physically motivated, nonempirical, and system dependent. The proposed functional yields ionization potentials, and fundamental and optical gaps of many, diverse molecular systems in excellent agreement with experiments, including organic and inorganic molecules and semiconducting nanocrystals. As a result, we further demonstrate that this hybrid functional gives the correct alignment between energy levels ofmore » the exemplary TTF-TCNQ donor-acceptor system.« less

Microsecond protein dynamics observed at the single-molecule level

NASA Astrophysics Data System (ADS)

Otosu, Takuhiro; Ishii, Kunihiko; Tahara, Tahei

2015-07-01

How polypeptide chains acquire specific conformations to realize unique biological functions is a central problem of protein science. Single-molecule spectroscopy, combined with fluorescence resonance energy transfer, is utilized to study the conformational heterogeneity and the state-to-state transition dynamics of proteins on the submillisecond to second timescales. However, observation of the dynamics on the microsecond timescale is still very challenging. This timescale is important because the elementary processes of protein dynamics take place and direct comparison between experiment and simulation is possible. Here we report a new single-molecule technique to reveal the microsecond structural dynamics of proteins through correlation of the fluorescence lifetime. This method, two-dimensional fluorescence lifetime correlation spectroscopy, is applied to clarify the conformational dynamics of cytochrome c. Three conformational ensembles and the microsecond transitions in each ensemble are indicated from the correlation signal, demonstrating the importance of quantifying microsecond dynamics of proteins on the folding free energy landscape.

Microsecond protein dynamics observed at the single-molecule level

PubMed Central

Otosu, Takuhiro; Ishii, Kunihiko; Tahara, Tahei

2015-01-01

How polypeptide chains acquire specific conformations to realize unique biological functions is a central problem of protein science. Single-molecule spectroscopy, combined with fluorescence resonance energy transfer, is utilized to study the conformational heterogeneity and the state-to-state transition dynamics of proteins on the submillisecond to second timescales. However, observation of the dynamics on the microsecond timescale is still very challenging. This timescale is important because the elementary processes of protein dynamics take place and direct comparison between experiment and simulation is possible. Here we report a new single-molecule technique to reveal the microsecond structural dynamics of proteins through correlation of the fluorescence lifetime. This method, two-dimensional fluorescence lifetime correlation spectroscopy, is applied to clarify the conformational dynamics of cytochrome c. Three conformational ensembles and the microsecond transitions in each ensemble are indicated from the correlation signal, demonstrating the importance of quantifying microsecond dynamics of proteins on the folding free energy landscape. PMID:26151767

Quasiparticle Approach to Molecules Interacting with Quantum Solvents.

PubMed

Lemeshko, Mikhail

2017-03-03

Understanding the behavior of molecules interacting with superfluid helium represents a formidable challenge and, in general, requires approaches relying on large-scale numerical simulations. Here, we demonstrate that experimental data collected over the last 20 years provide evidence that molecules immersed in superfluid helium form recently predicted angulon quasiparticles [Phys. Rev. Lett. 114, 203001 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.203001]. Most important, casting the many-body problem in terms of angulons amounts to a drastic simplification and yields effective molecular moments of inertia as straightforward analytic solutions of a simple microscopic Hamiltonian. The outcome of the angulon theory is in good agreement with experiment for a broad range of molecular impurities, from heavy to medium-mass to light species. These results pave the way to understanding molecular rotation in liquid and crystalline phases in terms of the angulon quasiparticle.

Integrated magnetic tweezers and single-molecule FRET for investigating the mechanical properties of nucleic acid.

PubMed

Long, Xi; Parks, Joseph W; Stone, Michael D

2016-08-01

Many enzymes promote structural changes in their nucleic acid substrates via application of piconewton forces over nanometer length scales. Magnetic tweezers (MT) is a single molecule force spectroscopy method widely used for studying the energetics of such mechanical processes. MT permits stable application of a wide range of forces and torques over long time scales with nanometer spatial resolution. However, in any force spectroscopy experiment, the ability to monitor structural changes in nucleic acids with nanometer sensitivity requires the system of interest to be held under high degrees of tension to improve signal to noise. This limitation prohibits measurement of structural changes within nucleic acids under physiologically relevant conditions of low stretching forces. To overcome this challenge, researchers have integrated a spatially sensitive fluorescence spectroscopy method, single molecule-FRET, with MT to allow simultaneous observation and manipulation of nanoscale structural transitions over a wide range of forces. Here, we describe a method for using this hybrid instrument to analyze the mechanical properties of nucleic acids. We expect that this method for analysis of nucleic acid structure will be easily adapted for experiments aiming to interrogate the mechanical responses of other biological macromolecules. Copyright © 2016 Elsevier Inc. All rights reserved.

Integrated magnetic tweezers and single-molecule FRET for investigating the mechanical properties of nucleic acid

PubMed Central

Long, Xi; Parks, Joseph W.; Stone, Michael D.

2017-01-01

Many enzymes promote structural changes in their nucleic acid substrates via application of piconewton forces over nanometer length scales. Magnetic tweezers (MT) is a single molecule force spectroscopy method widely used for studying the energetics of such mechanical processes. MT permits stable application of a wide range of forces and torques over long time scales with nanometer spatial resolution. However, in any force spectroscopy experiment, the ability to monitor structural changes in nucleic acids with nanometer sensitivity requires the system of interest to be held under high degrees of tension to improve signal to noise. This limitation prohibits measurement of structural changes within nucleic acids under physiologically relevant conditions of low stretching forces. To overcome this challenge, researchers have integrated a spatially sensitive fluorescence spectroscopy method, single molecule-FRET, with MT to allow simultaneous observation and manipulation of nanoscale structural transitions over a wide range of forces. Here, we describe a method for using this hybrid instrument to analyze the mechanical properties of nucleic acids. We expect that this method for analysis of nucleic acid structure will be easily adapted for experiments aiming to interrogate the mechanical responses of other biological macromolecules. PMID:27320203

Current status and future perspectives of electron interactions with molecules, clusters, surfaces, and interfaces [Workshop on Fundamental challenges in electron-driven chemistry; Workshop on Electron-driven processes: Scientific challenges and technological opportunities

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

Becker, Kurt H.; McCurdy, C. William; Orlando, Thomas M.

2000-09-01

This report is based largely on presentations and discussions at two workshops and contributions from workshop participants. The workshop on Fundamental Challenges in Electron-Driven Chemistry was held in Berkeley, October 9-10, 1998, and addressed questions regarding theory, computation, and simulation. The workshop on Electron-Driven Processes: Scientific Challenges and Technological Opportunities was held at Stevens Institute of Technology, March 16-17, 2000, and focused largely on experiments. Electron-molecule and electron-atom collisions initiate and drive almost all the relevant chemical processes associated with radiation chemistry, environmental chemistry, stability of waste repositories, plasma-enhanced chemical vapor deposition, plasma processing of materials for microelectronic devices andmore » other applications, and novel light sources for research purposes (e.g. excimer lamps in the extreme ultraviolet) and in everyday lighting applications. The life sciences are a rapidly advancing field where the important role of electron-driven processes is only now beginning to be recognized. Many of the applications of electron-initiated chemical processes require results in the near term. A large-scale, multidisciplinary and collaborative effort should be mounted to solve these problems in a timely way so that their solution will have the needed impact on the urgent questions of understanding the physico-chemical processes initiated and driven by electron interactions.« less

Classification of DNA nucleotides with transverse tunneling currents

NASA Astrophysics Data System (ADS)

Nyvold Pedersen, Jonas; Boynton, Paul; Di Ventra, Massimiliano; Jauho, Antti-Pekka; Flyvbjerg, Henrik

2017-01-01

It has been theoretically suggested and experimentally demonstrated that fast and low-cost sequencing of DNA, RNA, and peptide molecules might be achieved by passing such molecules between electrodes embedded in a nanochannel. The experimental realization of this scheme faces major challenges, however. In realistic liquid environments, typical currents in tunneling devices are of the order of picoamps. This corresponds to only six electrons per microsecond, and this number affects the integration time required to do current measurements in real experiments. This limits the speed of sequencing, though current fluctuations due to Brownian motion of the molecule average out during the required integration time. Moreover, data acquisition equipment introduces noise, and electronic filters create correlations in time-series data. We discuss how these effects must be included in the analysis of, e.g., the assignment of specific nucleobases to current signals. As the signals from different molecules overlap, unambiguous classification is impossible with a single measurement. We argue that the assignment of molecules to a signal is a standard pattern classification problem and calculation of the error rates is straightforward. The ideas presented here can be extended to other sequencing approaches of current interest.

Tracking the ultrafast motion of a single molecule by femtosecond orbital imaging

PubMed Central

Yu, Ping; Repp, Jascha; Huber, Rupert

2017-01-01

Watching a single molecule move on its intrinsic time scale—one of the central goals of modern nanoscience—calls for measurements that combine ultrafast temporal resolution1–8 with atomic spatial resolution9–30. Steady-state experiments achieve the requisite spatial resolution, as illustrated by direct imaging of individual molecular orbitals using scanning tunnelling microscopy9–11 or the acquisition of tip-enhanced Raman and luminescence spectra with sub-molecular resolution27–29. But tracking the dynamics of a single molecule directly in the time domain faces the challenge that single-molecule excitations need to be confined to an ultrashort time window. A first step towards overcoming this challenge has combined scanning tunnelling microscopy with so-called ‘lightwave electronics”1–8, which uses the oscillating carrier wave of tailored light pulses to directly manipulate electronic motion on time scales faster even than that of a single cycle of light. Here we use such ultrafast terahertz scanning tunnelling microscopy to access a state-selective tunnelling regime, where the peak of a terahertz electric-field waveform transiently opens an otherwise forbidden tunnelling channel through a single molecular state and thereby removes a single electron from an individual pentacene molecule’s highest occupied molecular orbital within a time window shorter than one oscillation cycle of the terahertz wave. We exploit this effect to record ~100 fs snapshot images of the structure of the orbital involved, and to reveal through pump-probe measurements coherent molecular vibrations at terahertz frequencies directly in the time domain and with sub-angstrom spatial resolution. We anticipate that the combination of lightwave electronics1–8 and atomic resolution of our approach will open the door to controlling electronic motion inside individual molecules at optical clock rates. PMID:27830788

Single Biomolecules at Cryogenic Temperatures: From Structure to Dynamics

NASA Astrophysics Data System (ADS)

Hofmann, Clemens; Kulzer, Florian; Zondervan, Rob; Köhler, Jürgen; Orrit, Michel

Elucidating the dynamics of proteins remains a central and daunting challenge of molecular biology. In our contribution we discuss the relevance of lowtemperature observations not only to structure, but also to dynamics, and thereby to the function of proteins. We first review investigations on light-harvesting complexes to illustrate how increased photostability at low temperatures and spectral selection provide a deeper insight into the excitonic interactions of the chromophores and the dynamics of the protein scaffold. Furthermore, we introduce a novel technique that achieves controlled, reproducible temperature cycles of a microscopic sample on microsecond timescales. We discuss the potential of this technique as a tool to achieve repeatable single-molecule freeze-trapping and to overcome some of the limitations of single-molecule experiments at room temperature.

Smart SERS Hot Spots: Single Molecules Can Be Positioned in a Plasmonic Nanojunction Using Host-Guest Chemistry.

PubMed

Kim, Nam Hoon; Hwang, Wooseup; Baek, Kangkyun; Rohman, Md Rumum; Kim, Jeehong; Kim, Hyun Woo; Mun, Jungho; Lee, So Young; Yun, Gyeongwon; Murray, James; Ha, Ji Won; Rho, Junsuk; Moskovits, Martin; Kim, Kimoon

2018-04-04

Single-molecule surface-enhanced Raman spectroscopy (SERS) offers new opportunities for exploring the complex chemical and biological processes that cannot be easily probed using ensemble techniques. However, the ability to place the single molecule of interest reliably within a hot spot, to enable its analysis at the single-molecule level, remains challenging. Here we describe a novel strategy for locating and securing a single target analyte in a SERS hot spot at a plasmonic nanojunction. The "smart" hot spot was generated by employing a thiol-functionalized cucurbit[6]uril (CB[6]) as a molecular spacer linking a silver nanoparticle to a metal substrate. This approach also permits one to study molecules chemically reluctant to enter the hot spot, by conjugating them to a moiety, such as spermine, that has a high affinity for CB[6]. The hot spot can accommodate at most a few, and often only a single, analyte molecule. Bianalyte experiments revealed that one can reproducibly treat the SERS substrate such that 96% of the hot spots contain a single analyte molecule. Furthermore, by utilizing a series of molecules each consisting of spermine bound to perylene bisimide, a bright SERS molecule, with polymethylene linkers of varying lengths, the SERS intensity as a function of distance from the center of the hot spot could be measured. The SERS enhancement was found to decrease as 1 over the square of the distance from the center of the hot spot, and the single-molecule SERS cross sections were found to increase with AgNP diameter.

Challenges and opportunities in absorption, distribution, metabolism, and excretion studies of therapeutic biologics.

PubMed

Xu, Xin; Vugmeyster, Yulia

2012-12-01

With the advancement of biotechnology in the last two decades, optimized and novel modalities and platforms of biologic moieties have emerged rapidly in drug discovery pipelines. In addition, new technologies for delivering therapeutic biologics (e.g., needle-free devices, nanoparticle complexes), as well as novel approaches for disease treatments (e.g., stem cell therapy, individualized medicine), continue to be developed. While pharmacokinetic studies are routinely carried out for therapeutic biologics, experiments that elucidate underlying mechanisms for clearance and biodistribution or identify key factors that govern absorption, distribution, metabolism, and excretion (ADME) of biologics often are not thoroughly conducted. Realizing the importance of biologics as therapeutic agents, pharmaceutical industry has recently begun to move the research focus from small molecules only to a blended portfolio consisting of both small molecules and biologics. This trend brings many opportunities for scientists working in the drug disposition research field. In anticipation of these opportunities and associated challenges, this review highlights impact of ADME studies on clinical and commercial success of biologics, with a particular focus on emerging applications and technologies and linkage with mechanistic pharmacokinetic/pharmacodynamic modeling and biomarker research.

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

Small Molecule Sequential Dual-Targeting Theragnostic Strategy (SMSDTTS): from Preclinical Experiments towards Possible Clinical Anticancer Applications

PubMed Central

Li, Junjie; Oyen, Raymond; Verbruggen, Alfons; Ni, Yicheng

2013-01-01

Hitting the evasive tumor cells proves challenging in targeted cancer therapies. A general and unconventional anticancer approach namely small molecule sequential dual-targeting theragnostic strategy (SMSDTTS) has recently been introduced with the aims to target and debulk the tumor mass, wipe out the residual tumor cells, and meanwhile enable cancer detectability. This dual targeting approach works in two steps for systemic delivery of two naturally derived drugs. First, an anti-tubulin vascular disrupting agent, e.g., combretastatin A4 phosphate (CA4P), is injected to selectively cut off tumor blood supply and to cause massive necrosis, which nevertheless always leaves peripheral tumor residues. Secondly, a necrosis-avid radiopharmaceutical, namely 131I-hypericin (131I-Hyp), is administered the next day, which accumulates in intratumoral necrosis and irradiates the residual cancer cells with beta particles. Theoretically, this complementary targeted approach may biologically and radioactively ablate solid tumors and reduce the risk of local recurrence, remote metastases, and thus cancer mortality. Meanwhile, the emitted gamma rays facilitate radio-scintigraphy to detect tumors and follow up the therapy, hence a simultaneous theragnostic approach. SMSDTTS has now shown promise from multicenter animal experiments and may demonstrate unique anticancer efficacy in upcoming preliminary clinical trials. In this short review article, information about the two involved agents, the rationale of SMSDTTS, its preclinical antitumor efficacy, multifocal targetability, simultaneous theragnostic property, and toxicities of the dose regimens are summarized. Meanwhile, possible drawbacks, practical challenges and future improvement with SMSDTTS are discussed, which hopefully may help to push forward this strategy from preclinical experiments towards possible clinical applications. PMID:23412554

Small Molecule Sequential Dual-Targeting Theragnostic Strategy (SMSDTTS): from Preclinical Experiments towards Possible Clinical Anticancer Applications.

PubMed

Li, Junjie; Oyen, Raymond; Verbruggen, Alfons; Ni, Yicheng

2013-01-01

Hitting the evasive tumor cells proves challenging in targeted cancer therapies. A general and unconventional anticancer approach namely small molecule sequential dual-targeting theragnostic strategy (SMSDTTS) has recently been introduced with the aims to target and debulk the tumor mass, wipe out the residual tumor cells, and meanwhile enable cancer detectability. This dual targeting approach works in two steps for systemic delivery of two naturally derived drugs. First, an anti-tubulin vascular disrupting agent, e.g., combretastatin A4 phosphate (CA4P), is injected to selectively cut off tumor blood supply and to cause massive necrosis, which nevertheless always leaves peripheral tumor residues. Secondly, a necrosis-avid radiopharmaceutical, namely (131)I-hypericin ((131)I-Hyp), is administered the next day, which accumulates in intratumoral necrosis and irradiates the residual cancer cells with beta particles. Theoretically, this complementary targeted approach may biologically and radioactively ablate solid tumors and reduce the risk of local recurrence, remote metastases, and thus cancer mortality. Meanwhile, the emitted gamma rays facilitate radio-scintigraphy to detect tumors and follow up the therapy, hence a simultaneous theragnostic approach. SMSDTTS has now shown promise from multicenter animal experiments and may demonstrate unique anticancer efficacy in upcoming preliminary clinical trials. In this short review article, information about the two involved agents, the rationale of SMSDTTS, its preclinical antitumor efficacy, multifocal targetability, simultaneous theragnostic property, and toxicities of the dose regimens are summarized. Meanwhile, possible drawbacks, practical challenges and future improvement with SMSDTTS are discussed, which hopefully may help to push forward this strategy from preclinical experiments towards possible clinical applications.

Understanding the Conductance of Single-Molecule Junctions from First Principles

NASA Astrophysics Data System (ADS)

Quek, Su Ying

2008-03-01

Discovering the anatomy of single-molecule junctions, in order to exploit their transport behavior, poses fundamental challenges to nanoscience. First-principles calculations based on density-functional theory (DFT) can, together with experiment, provide detailed atomic-scale insights into the transport properties, and their relation to junction structure and electronic properties. Here, a DFT scattering state approach [1] is used to explore the single-molecule conductance of two prototypical junctions as a function of junction geometry, in the context of recent experiments. First, the computed conductance of 15 distinct benzene-diamine-Au junctions is compared to a large robust experimental data set [2]. The amine-gold bonding is shown to be highly selective, but flexible, resulting in a conductance that is insensitive to other details of the junction structure. The range of computed conductance corresponds well to the narrow distribution in experiment, although the average calculated conductance is approximately 7 times larger. This discrepancy is attributed to the absence of many-electron corrections in the DFT molecular orbital energies; a simple physically-motivated estimate for the self-energy corrections results in a conductance that is much closer to experiment [3]. Second, similar first-principles techniques are applied to a range of bipyridine-Au junctions. The extent to which Au-pyridine link bonding is affected by the constraints of forming bipyridine-Au junctions is investigated. In some contrast to the amine case, the computed conductance shows a strong sensitivity to the tilt of the bipyridine rings relative to the Au surfaces. Experiments probing the conductance of bipyridine-Au junctions are discussed in the context of these findings. [1] H. J. Choi et al, Phys Rev B, 76, 155420 (2007) [2] L. Venkataraman et al, Nano Lett 6, 458 (2006) [3] S. Y. Quek et al, Nano Lett. 7, 3477 (2007)

Connecting Lab-Based Attosecond Science with FEL research

ScienceCinema

Vrakking, Marc

2017-12-09

In the last few years laboratory-scale femtosecond laser-based research using XUV light has developed dramatically following the successful development of attosecond laser pulses by means of high-harmonic generation. Using attosecond laser pulses, studies of electron dynamics on the natural timescale that electronic processes occur in atoms, molecules and solids can be contemplated, providing unprecedented insight into the fundamental role that electrons play in photo-induced processes. In my talk I will briefly review the present status of the attosecond science research field in terms of present and foreseen capabilities, and discuss a few recent applications, including a first example of the use of attosecond laser pulses in molecular science. In addition, I will discuss very recent results of experiments where photoionization of dynamically aligned molecules is investigated using a high-harmonics XUV source. Photoionization of aligned molecules becomes all the more interesting if the experiment is performed using x-ray photons. Following the absorption of x-rays, ejected photoelectrons can be used as a probe of the (time-evolving) molecular structure, making use of intra-molecular electron diffraction. This amounts, as some have stated, to “illuminating the molecule from within”. I will present the present status of our experiments on this topic making use of the FLASH free electron laser in Hamburg. Future progress in this research field not only depends on the availability of better and more powerful light sources, but also requires sophisticated detector strategies. In my talk I will explain how we are trying to meet some of the experimental challenges by using the Medipix family of detectors, which we have already used for time- and space-resolved imaging of electrons and ions.

Electron transport in molecular wires with transition metal contacts

NASA Astrophysics Data System (ADS)

Dalgleish, Hugh

A molecular wire is an organic molecule that forms a conducting bridge between electronic contacts. Single molecules are likely to be the smallest entities to conduct electricity and thus molecular wires present many interesting challenges to fundamental science as well as enormous potential for nanoelectronic technological applications. A particular challenge stems from the realization that the properties of molecular wires are strongly influenced by the combined characteristics of the molecule and the metal contacts. While gold has been the most studied contact material to date, interest in molecular wires with transition metal contacts that are electronically more complex than gold is growing. This thesis presents a theoretical investigation of electron transport and associated phenomena in molecular wires with transition metal contacts. An appropriate methodology is developed on the basis of Landauer theory and ab initio and semi-empirical considerations and new, physically important systems are identified. Spin-dependent transport mechanisms and device characteristics are explored for molecular wires with ferromagnetic iron contacts, systems that have not been considered previously, either theoretically or experimentally. Electron transport between iron point contacts bridged by iron atoms is also investigated. Spin-dependent transport is also studied for molecules bridging nickel contacts and a possible explanation of some experimentally observed phenomena is proposed. A novel physical phenomenon termed strong spin current rectification and a new controllable negative differential resistance mechanism with potential applications for molecular electronic technology are introduced. The phenomena predicted in this thesis should be accessible to present day experimental techniques and this work is intended to stimulate experiments directed at observing them. Keywords. molecular electronics; spintronics; electron transport; interface states.

Rapid parameterization of small molecules using the Force Field Toolkit.

PubMed

Mayne, Christopher G; Saam, Jan; Schulten, Klaus; Tajkhorshid, Emad; Gumbart, James C

2013-12-15

The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics simulations to many biological systems of interest, especially in fields such as drug discovery. Although the release of generalized versions of common classical force fields, for example, General Amber Force Field and CHARMM General Force Field, have posited guidelines for parameterization of small molecules, many technical challenges remain that have hampered their wide-scale extension. The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error-prone tasks, and graphical user interface design. Distributed as a VMD plugin, ffTK facilitates the traversal of a clear and organized workflow resulting in a complete set of CHARMM-compatible parameters. A variety of tools are provided to generate quantum mechanical target data, setup multidimensional optimization routines, and analyze parameter performance. Parameters developed for a small test set of molecules using ffTK were comparable to existing CGenFF parameters in their ability to reproduce experimentally measured values for pure-solvent properties (<15% error from experiment) and free energy of solvation (±0.5 kcal/mol from experiment). Copyright © 2013 Wiley Periodicals, Inc.

Catalysis for Fluorination and Trifluoromethylation

PubMed Central

Furuya, Takeru; Kamlet, Adam S.; Ritter, Tobias

2011-01-01

Preface Recent advances in catalysis have made the incorporation of fluorine into complex organic molecules easier than ever before, but selective, general, and practical fluorination reactions remain sought after. Fluorination of molecules often imparts desirable properties such as metabolic and thermal stability, and fluorinated molecules are therefore frequently used as pharmaceuticals or materials. Even with the latest advances in chemistry, carbon–fluorine bond formation in complex molecules is still a significant challenge. Within the last few years, new reactions to make organofluorides have emerged and exemplify how to overcome some of the intricate challenges associated with fluorination. PMID:21614074

Towards first-principles calculation of electronic excitations in the ring of the protein-bound bacteriochlorophylls

NASA Astrophysics Data System (ADS)

Polyakov, Igor V.; Khrenova, Maria G.; Moskovsky, Alexander A.; Shabanov, Boris M.; Nemukhin, Alexander V.

2018-04-01

Modeling electronic excitation of bacteriochlorophyll (BChl) molecules in light-harvesting (LH) antennae from photosynthetic centers presents a challenge for the quantum theory. We report on a quantum chemical study of the ring of 32 BChl molecules from the bacterial core complex LH1-RC. Diagonal and off-diagonal elements of the excitonic Hamiltonian matrices are estimated in quantum chemical calculations of relevant fragments using the TD-DFT and CIS approaches. The deviation of the computed excitation energy of this BChl system from the experimental data related to the Qy band maximum of this LH1-RC complex is about 0.2 eV. We demonstrate that corrections due to improvement in modeling of an individual BChl molecule and due to contributions from the protein environment are in the range of the obtained discrepancy between theory and experiment. Differences between results of the excitonic model and direct quantum chemical calculations of BChl aggregates fall in the same range.

FAST CARS: Engineering a laser spectroscopic technique for rapid identification of bacterial spores

PubMed Central

Scully, M. O.; Kattawar, G. W.; Lucht, R. P.; Opatrný, T.; Pilloff, H.; Rebane, A.; Sokolov, A. V.; Zubairy, M. S.

2002-01-01

Airborne contaminants, e.g., bacterial spores, are usually analyzed by time-consuming microscopic, chemical, and biological assays. Current research into real-time laser spectroscopic detectors of such contaminants is based on e.g., resonance fluorescence. The present approach derives from recent experiments in which atoms and molecules are prepared by one (or more) coherent laser(s) and probed by another set of lasers. However, generating and using maximally coherent oscillation in macromolecules having an enormous number of degrees of freedom is challenging. In particular, the short dephasing times and rapid internal conversion rates are major obstacles. However, adiabatic fast passage techniques and the ability to generate combs of phase-coherent femtosecond pulses provide tools for the generation and utilization of maximal quantum coherence in large molecules and biopolymers. We call this technique FAST CARS (femtosecond adaptive spectroscopic techniques for coherent anti-Stokes Raman spectroscopy), and the present article proposes and analyses ways in which it could be used to rapidly identify preselected molecules in real time. PMID:12177405

Real-time molecular scale observation of crystal formation.

PubMed

Schreiber, Roy E; Houben, Lothar; Wolf, Sharon G; Leitus, Gregory; Lang, Zhong-Ling; Carbó, Jorge J; Poblet, Josep M; Neumann, Ronny

2017-04-01

How molecules in solution form crystal nuclei, which then grow into large crystals, is a poorly understood phenomenon. The classical mechanism of homogeneous crystal nucleation proceeds via the spontaneous random aggregation of species from liquid or solution. However, a non-classical mechanism suggests the formation of an amorphous dense phase that reorders to form stable crystal nuclei. So far it has remained an experimental challenge to observe the formation of crystal nuclei from five to thirty molecules. Here, using polyoxometallates, we show that the formation of small crystal nuclei is observable by cryogenic transmission electron microscopy. We observe both classical and non-classical nucleation processes, depending on the identity of the cation present. The experiments verify theoretical studies that suggest non-classical nucleation is the lower of the two energy pathways. The arrangement in just a seven-molecule proto-crystal matches the order found by X-ray diffraction of a single bulk crystal, which demonstrates that the same structure was formed in each case.

Capturing Guest Dynamics in Metal-Organic Framework CPO-27-M (M = Mg, Zn) by (2)H Solid-State NMR Spectroscopy.

PubMed

Xu, Jun; Sinelnikov, Regina; Huang, Yining

2016-06-07

Metal-organic frameworks (MOFs) are promising porous materials for gas separation and storage as well as sensing. In particular, a series of isostructural MOFs with coordinately unsaturated metal centers, namely, CPO-27-M or M-MOF-74 (M = Mg, Zn, Mn, Fe, Ni, Co, Cu), have shown exceptional adsorption capacity and selectivity compared to those of classical MOFs that contain only fully coordinated metal sites. Although it is widely accepted that the interaction between guest molecules and exposed metal centers is responsible for good selectivity and large maximum uptake, the investigation of such guest-metal interaction is very challenging because adsorbed molecules are usually disordered in the pores and undergo rapid thermal motions. (2)H solid-state NMR (SSNMR) spectroscopy is one of the most extensively used techniques for capturing guest dynamics in porous materials. In this work, variable-temperature (2)H wide-line SSNMR experiments were performed on CPO-27-M (M = Mg, Zn) loaded with four prototypical guest molecules: D2O, CD3CN, acetone-d6, and C6D6. The results indicate that different guest molecules possess distinct dynamic behaviors inside the channel of CPO-27-M. For a given guest molecule, its dynamic behavior also depends on the nature of the metal centers. The binding strength of guest molecules is discussed on the basis of the (2)H SSNMR data.

Chess games: a model for RNA based computation.

PubMed

Cukras, A R; Faulhammer, D; Lipton, R J; Landweber, L F

1999-10-01

Here we develop the theory of RNA computing and a method for solving the 'knight problem' as an instance of a satisfiability (SAT) problem. Using only biological molecules and enzymes as tools, we developed an algorithm for solving the knight problem (3 x 3 chess board) using a 10-bit combinatorial pool and sequential RNase H digestions. The results of preliminary experiments presented here reveal that the protocol recovers far more correct solutions than expected at random, but the persistence of errors still presents the greatest challenge.

'Single molecule': theory and experiments, an introduction

PubMed Central

2013-01-01

At scales below micrometers, Brownian motion dictates most of the behaviors. The simple observation of a colloid is striking: a permanent and random motion is seen, whereas inertial forces play a negligible role. This Physics, where velocity is proportional to force, has opened new horizons in biology. The random feature is challenged in living systems where some proteins - molecular motors - have a directed motion whereas their passive behaviors of colloid should lead to a Brownian motion. Individual proteins, polymers of living matter such as DNA, RNA, actin or microtubules, molecular motors, all these objects can be viewed as chains of colloids. They are submitted to shocks from molecules of the solvent. Shapes taken by these biopolymers or dynamics imposed by motors can be measured and modeled from single molecules to their collective effects. Thanks to the development of experimental methods such as optical tweezers, Atomic Force Microscope (AFM), micropipettes, and quantitative fluorescence (such as Förster Resonance Energy Transfer, FRET), it is possible to manipulate these individual biomolecules in an unprecedented manner: experiments allow to probe the validity of models; and a new Physics has thereby emerged with original biological insights. Theories based on statistical mechanics are needed to explain behaviors of these systems. When force-extension curves of these molecules are extracted, the curves need to be fitted with models that predict the deformation of free objects or submitted to a force. When velocity of motors is altered, a quantitative analysis is required to explain the motions of individual molecules under external forces. This lecture will give some elements of introduction to the lectures of the session 'Nanophysics for Molecular Biology'. PMID:24565227

Small Molecule Chemical Probes of MicroRNA Function

PubMed Central

Velagapudi, Sai Pradeep; Vummidi, Balayeshwanth R.; Disney, Matthew D.

2015-01-01

MicroRNAs (miRNAs) are small, non-coding RNAs that control protein expression. Aberrant miRNA expression has been linked to various human diseases, and thus miRNAs have been explored as diagnostic markers and therapeutic targets. Although it is challenging to target RNA with small molecules in general, there have been successful campaigns that have identified small molecule modulators of miRNA function by targeting various pathways. For example, small molecules that modulate transcription and target nuclease processing sites in miRNA precursors have been identified. Herein, we describe challenges in developing chemical probes that target miRNAs and highlight aspects of miRNA cellular biology elucidated by using small molecule chemical probes. We expect that this area will expand dramatically in the near future as strides are made to understand small molecule recognition of RNA from a fundamental perspective. PMID:25500006

BFPTool: a software tool for analysis of Biomembrane Force Probe experiments.

PubMed

Šmít, Daniel; Fouquet, Coralie; Doulazmi, Mohamed; Pincet, Frédéric; Trembleau, Alain; Zapotocky, Martin

2017-01-01

The Biomembrane Force Probe is an approachable experimental technique commonly used for single-molecule force spectroscopy and experiments on biological interfaces. The technique operates in the range of forces from 0.1 pN to 1000 pN. Experiments are typically repeated many times, conditions are often not optimal, the captured video can be unstable and lose focus; this makes efficient analysis challenging, while out-of-the-box non-proprietary solutions are not freely available. This dedicated tool was developed to integrate and simplify the image processing and analysis of videomicroscopy recordings from BFP experiments. A novel processing feature, allowing the tracking of the pipette, was incorporated to address a limitation of preceding methods. Emphasis was placed on versatility and comprehensible user interface implemented in a graphical form. An integrated analytical tool was implemented to provide a faster, simpler and more convenient way to process and analyse BFP experiments.

Vibronic transitions in the alkali-metal (Li, Na, K, Rb) - alkaline-earth-metal (Ca, Sr) series: A systematic analysis of de-excitation mechanisms based on the graphical mapping of Frank-Condon integrals

NASA Astrophysics Data System (ADS)

Pototschnig, Johann V.; Meyer, Ralf; Hauser, Andreas W.; Ernst, Wolfgang E.

2017-02-01

Research on ultracold molecules has seen a growing interest recently in the context of high-resolution spectroscopy and quantum computation. After forming weakly bound molecules from atoms in cold collisions, the preparation of molecules in low vibrational levels of the ground state is experimentally challenging, and typically achieved by population transfer using excited electronic states. Accurate potential energy surfaces are needed for a correct description of processes such as the coherent de-excitation from the highest and therefore weakly bound vibrational levels in the electronic ground state via couplings to electronically excited states. This paper is dedicated to the vibrational analysis of potentially relevant electronically excited states in the alkali-metal (Li, Na, K, Rb)- alkaline-earth metal (Ca,Sr) diatomic series. Graphical maps of Frank-Condon overlap integrals are presented for all molecules of the group. By comparison to overlap graphics produced for idealized potential surfaces, we judge the usability of the selected states for future experiments on laser-enhanced molecular formation from mixtures of quantum degenerate gases.

Fit Point-Wise AB Initio Calculation Potential Energies to a Multi-Dimension Long-Range Model

NASA Astrophysics Data System (ADS)

Zhai, Yu; Li, Hui; Le Roy, Robert J.

2016-06-01

A potential energy surface (PES) is a fundamental tool and source of understanding for theoretical spectroscopy and for dynamical simulations. Making correct assignments for high-resolution rovibrational spectra of floppy polyatomic and van der Waals molecules often relies heavily on predictions generated from a high quality ab initio potential energy surface. Moreover, having an effective analytic model to represent such surfaces can be as important as the ab initio results themselves. For the one-dimensional potentials of diatomic molecules, the most successful such model to date is arguably the ``Morse/Long-Range'' (MLR) function developed by R. J. Le Roy and coworkers. It is very flexible, is everywhere differentiable to all orders. It incorporates correct predicted long-range behaviour, extrapolates sensibly at both large and small distances, and two of its defining parameters are always the physically meaningful well depth {D}_e and equilibrium distance r_e. Extensions of this model, called the Multi-Dimension Morse/Long-Range (MD-MLR) function, linear molecule-linear molecule systems and atom-non-linear molecule system. have been applied successfully to atom-plus-linear molecule, linear molecule-linear molecule and atom-non-linear molecule systems. However, there are several technical challenges faced in modelling the interactions of general molecule-molecule systems, such as the absence of radial minima for some relative alignments, difficulties in fitting short-range potential energies, and challenges in determining relative-orientation dependent long-range coefficients. This talk will illustrate some of these challenges and describe our ongoing work in addressing them. Mol. Phys. 105, 663 (2007); J. Chem. Phys. 131, 204309 (2009); Mol. Phys. 109, 435 (2011). Phys. Chem. Chem. Phys. 10, 4128 (2008); J. Chem. Phys. 130, 144305 (2009) J. Chem. Phys. 132, 214309 (2010) J. Chem. Phys. 140, 214309 (2010)

Integrated multiscale biomaterials experiment and modelling: a perspective

PubMed Central

Buehler, Markus J.; Genin, Guy M.

2016-01-01

Advances in multiscale models and computational power have enabled a broad toolset to predict how molecules, cells, tissues and organs behave and develop. A key theme in biological systems is the emergence of macroscale behaviour from collective behaviours across a range of length and timescales, and a key element of these models is therefore hierarchical simulation. However, this predictive capacity has far outstripped our ability to validate predictions experimentally, particularly when multiple hierarchical levels are involved. The state of the art represents careful integration of multiscale experiment and modelling, and yields not only validation, but also insights into deformation and relaxation mechanisms across scales. We present here a sampling of key results that highlight both challenges and opportunities for integrated multiscale experiment and modelling in biological systems. PMID:28981126

Going clean: structure and dynamics of peptides in the gas phase and paths to solvation.

PubMed

Baldauf, Carsten; Rossi, Mariana

2015-12-16

The gas phase is an artificial environment for biomolecules that has gained much attention both experimentally and theoretically due to its unique characteristic of providing a clean room environment for the comparison between theory and experiment. In this review we give an overview mainly on first-principles simulations of isolated peptides and the initial steps of their interactions with ions and solvent molecules: a bottom up approach to the complexity of biological environments. We focus on the accuracy of different methods to explore the conformational space, the connections between theory and experiment regarding collision cross section evaluations and (anharmonic) vibrational spectra, and the challenges faced in this field.

Small molecule chemical probes of microRNA function.

PubMed

Velagapudi, Sai Pradeep; Vummidi, Balayeshwanth R; Disney, Matthew D

2015-02-01

MicroRNAs (miRNAs) are small, non-coding RNAs that control protein expression. Aberrant miRNA expression has been linked to various human diseases, and thus miRNAs have been explored as diagnostic markers and therapeutic targets. Although it is challenging to target RNA with small molecules in general, there have been successful campaigns that have identified small molecule modulators of miRNA function by targeting various pathways. For example, small molecules that modulate transcription and target nuclease processing sites in miRNA precursors have been identified. Herein, we describe challenges in developing chemical probes that target miRNAs and highlight aspects of miRNA cellular biology elucidated by using small molecule chemical probes. We expect that this area will expand dramatically in the near future as progress is made in understanding small molecule recognition of RNA. Copyright © 2014. Published by Elsevier Ltd.

Rational design of chemical genetic probes of RNA function and lead therapeutics targeting repeating transcripts.

PubMed

Disney, Matthew D

2013-12-01

RNA is an important yet vastly underexploited target for small molecule chemical probes or lead therapeutics. Small molecules have been used successfully to modulate the function of the bacterial ribosome, viral RNAs and riboswitches. These RNAs are either highly expressed or can be targeted using substrate mimicry, a mainstay in the design of enzyme inhibitors. However, most cellular RNAs are neither highly expressed nor have a lead small molecule inhibitor, a significant challenge for drug discovery efforts. Herein, I describe the design of small molecules targeting expanded repeating transcripts that cause myotonic muscular dystrophy (DM). These test cases illustrate the challenges of designing small molecules that target RNA and the advantages of targeting repeating transcripts. Lastly, I discuss how small molecules might be more advantageous than oligonucleotides for targeting RNA. Copyright © 2013 Elsevier Ltd. All rights reserved.

The Carbon-Water Interface: Modeling Challenges and Opportunities for the Water-Energy Nexus.

PubMed

Striolo, Alberto; Michaelides, Angelos; Joly, Laurent

2016-06-07

Providing clean water and sufficient affordable energy to all without compromising the environment is a key priority in the scientific community. Many recent studies have focused on carbon-based devices in the hope of addressing this grand challenge, justifying and motivating detailed studies of water in contact with carbonaceous materials. Such studies are becoming increasingly important because of the miniaturization of newly proposed devices, with ubiquitous nanopores, large surface-to-volume ratio, and many, perhaps most of the water molecules in contact with a carbon-based surface. In this brief review, we discuss some recent advances obtained via simulations and experiments in the development of carbon-based materials for applications in water desalination. We suggest possible ways forward, with particular emphasis on the synergistic combination of experiments and simulations, with simulations now sometimes offering sufficient accuracy to provide fundamental insights. We also point the interested reader to recent works that complement our short summary on the state of the art of this important and fascinating field.

Chemical Topic Modeling: Exploring Molecular Data Sets Using a Common Text-Mining Approach.

PubMed

Schneider, Nadine; Fechner, Nikolas; Landrum, Gregory A; Stiefl, Nikolaus

2017-08-28

Big data is one of the key transformative factors which increasingly influences all aspects of modern life. Although this transformation brings vast opportunities it also generates novel challenges, not the least of which is organizing and searching this data deluge. The field of medicinal chemistry is not different: more and more data are being generated, for instance, by technologies such as DNA encoded libraries, peptide libraries, text mining of large literature corpora, and new in silico enumeration methods. Handling those huge sets of molecules effectively is quite challenging and requires compromises that often come at the expense of the interpretability of the results. In order to find an intuitive and meaningful approach to organizing large molecular data sets, we adopted a probabilistic framework called "topic modeling" from the text-mining field. Here we present the first chemistry-related implementation of this method, which allows large molecule sets to be assigned to "chemical topics" and investigating the relationships between those. In this first study, we thoroughly evaluate this novel method in different experiments and discuss both its disadvantages and advantages. We show very promising results in reproducing human-assigned concepts using the approach to identify and retrieve chemical series from sets of molecules. We have also created an intuitive visualization of the chemical topics output by the algorithm. This is a huge benefit compared to other unsupervised machine-learning methods, like clustering, which are commonly used to group sets of molecules. Finally, we applied the new method to the 1.6 million molecules of the ChEMBL22 data set to test its robustness and efficiency. In about 1 h we built a 100-topic model of this large data set in which we could identify interesting topics like "proteins", "DNA", or "steroids". Along with this publication we provide our data sets and an open-source implementation of the new method (CheTo) which will be part of an upcoming version of the open-source cheminformatics toolkit RDKit.

Vibrational Heat Transport in Molecular Junctions

NASA Astrophysics Data System (ADS)

Segal, Dvira; Agarwalla, Bijay Kumar

2016-05-01

We review studies of vibrational energy transfer in a molecular junction geometry, consisting of a molecule bridging two heat reservoirs, solids or large chemical compounds. This setup is of interest for applications in molecular electronics, thermoelectrics, and nanophononics, and for addressing basic questions in the theory of classical and quantum transport. Calculations show that system size, disorder, structure, dimensionality, internal anharmonicities, contact interaction, and quantum coherent effects are factors that combine to determine the predominant mechanism (ballistic/diffusive), effectiveness (poor/good), and functionality (linear/nonlinear) of thermal conduction at the nanoscale. We review recent experiments and relevant calculations of quantum heat transfer in molecular junctions. We recount the Landauer approach, appropriate for the study of elastic (harmonic) phononic transport, and outline techniques that incorporate molecular anharmonicities. Theoretical methods are described along with examples illustrating the challenge of reaching control over vibrational heat conduction in molecules.

Simultaneous AFM topography and recognition imaging at the plasma membrane of mammalian cells.

PubMed

Chtcheglova, Lilia A; Hinterdorfer, Peter

2018-01-01

Elucidation the nano-organization of membrane proteins at/within the plasma membrane is probably the most demanding and still challenging task in cell biology since requires experimental approaches with nanoscale resolution. During last decade, atomic force microscopy (AFM)-based simultaneous topography and recognition imaging (TREC) has become a powerful tool to quickly obtain local receptor nano-maps on complex heterogeneous biosurfaces such as cells and membranes. Here we emphasize the TREC technique and explain how to unravel the nano-landscape of mammalian cells. We describe the procedures for all steps of the experiment including tip functionalization with ligand molecules, sample preparation, and localization of key molecules on the cell surface. We also discuss the current limitations and future perspectives of this technique. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Femtosecond characterization of vibrational optical activity of chiral molecules.

PubMed

Rhee, Hanju; June, Young-Gun; Lee, Jang-Soo; Lee, Kyung-Koo; Ha, Jeong-Hyon; Kim, Zee Hwan; Jeon, Seung-Joon; Cho, Minhaeng

2009-03-19

Optical activity is the result of chiral molecules interacting differently with left versus right circularly polarized light. Because of this intrinsic link to molecular structure, the determination of optical activity through circular dichroism (CD) spectroscopy has long served as a routine method for obtaining structural information about chemical and biological systems in condensed phases. A recent development is time-resolved CD spectroscopy, which can in principle map the structural changes associated with biomolecular function and thus lead to mechanistic insights into fundamental biological processes. But implementing time-resolved CD measurements is experimentally challenging because CD is a notoriously weak effect (a factor of 10(-4)-10(-6) smaller than absorption). In fact, this problem has so far prevented time-resolved vibrational CD experiments. Here we show that vibrational CD spectroscopy with femtosecond time resolution can be realized when using heterodyned spectral interferometry to detect the phase and amplitude of the infrared optical activity free-induction-decay field in time (much like in a pulsed NMR experiment). We show that we can detect extremely weak signals in the presence of large achiral background contributions, by simultaneously measuring with a femtosecond laser pulse the vibrational CD and optical rotatory dispersion spectra of dissolved chiral limonene molecules. We have so far only targeted molecules in equilibrium, but it would be straightforward to extend the method for the observation of ultrafast structural changes such as those occurring during protein folding or asymmetric chemical reactions. That is, we should now be in a position to produce 'molecular motion pictures' of fundamental molecular processes from a chiral perspective.

Syntheses, Characterizations, and Applications of Molecular Metal Wires and Functional Nanomaterials

DTIC Science & Technology

2009-12-22

challenges Conductance of single molecules Concluding Remarks...values of single -molecule conductance for such pentaruthenium EMACs, other triruthenium and trirhodium EMACs (Dalton Trans. 2009, 2623) were obtained...a voltage-activated switch, or a single -molecule transistor. Among the molecules reported in this research field,1 EMACs2 are particularly

Prediction of new bioactive molecules using a Bayesian belief network.

PubMed

Abdo, Ammar; Leclère, Valérie; Jacques, Philippe; Salim, Naomie; Pupin, Maude

2014-01-27

Natural products and synthetic compounds are a valuable source of new small molecules leading to novel drugs to cure diseases. However identifying new biologically active small molecules is still a challenge. In this paper, we introduce a new activity prediction approach using Bayesian belief network for classification (BBNC). The roots of the network are the fragments composing a compound. The leaves are, on one side, the activities to predict and, on another side, the unknown compound. The activities are represented by sets of known compounds, and sets of inactive compounds are also used. We calculated a similarity between an unknown compound and each activity class. The more similar activity is assigned to the unknown compound. We applied this new approach on eight well-known data sets extracted from the literature and compared its performance to three classical machine learning algorithms. Experiments showed that BBNC provides interesting prediction rates (from 79% accuracy for high diverse data sets to 99% for low diverse ones) with a short time calculation. Experiments also showed that BBNC is particularly effective for homogeneous data sets but has been found to perform less well with structurally heterogeneous sets. However, it is important to stress that we believe that using several approaches whenever possible for activity prediction can often give a broader understanding of the data than using only one approach alone. Thus, BBNC is a useful addition to the computational chemist's toolbox.

Controllable atomistic graphene oxide model and its application in hydrogen sulfide removal.

PubMed

Huang, Liangliang; Seredych, Mykola; Bandosz, Teresa J; van Duin, Adri C T; Lu, Xiaohua; Gubbins, Keith E

2013-11-21

The determination of an atomistic graphene oxide (GO) model has been challenging due to the structural dependence on different synthesis methods. In this work we combine temperature-programmed molecular dynamics simulation techniques and the ReaxFF reactive force field to generate realistic atomistic GO structures. By grafting a mixture of epoxy and hydroxyl groups to the basal graphene surface and fine-tuning their initial concentrations, we produce in a controllable manner the GO structures with different functional groups and defects. The models agree with structural experimental data and with other ab initio quantum calculations. Using the generated atomistic models, we perform reactive adsorption calculations for H2S and H2O∕H2S mixtures on GO materials and compare the results with experiment. We find that H2S molecules dissociate on the carbonyl functional groups, and H2O, CO2, and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H2O∕H2S mixtures, H2O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H2S decomposition. The calculation agrees well with the experiments. The methodology and the procedure applied in this work open a new door to the theoretical studies of GO and can be extended to the research on other amorphous materials.

Transition from Gaseous Compounds to Aerosols in Titan's Atmosphere

NASA Technical Reports Server (NTRS)

Lebonnois, Sebastien; Bakes, E. L. O.; McKay, Christopher P.; DeVincenzi, Donald (Technical Monitor)

2002-01-01

We investigate the chemical transition of simple molecules like C2H2 and HCN into aerosol particles in the context of Titan's atmosphere. Experiments that synthesize analogs (tholins) for these aerosols can help understand and constrain these polymerization mechanisms. Using information available from these experiments, we suggest chemical pathways that can link simple molecules to macromolecules, that will be the precursors to aerosol particles: polymers of acetylene and cyanoacetylene, polycyclic aromatics (PAHs), polymers of HCN and other nitriles, and polynes. Although our goal here is not to build a detailed kinetic model for this transition, we propose parameterizations to estimate the production rates of these macromolecules, their C/N and C/H ratios, and the loss of parent molecules (C2H2, HCN, HC3N and other nitriles, C6H6) from the gas phase to the haze. We use a 1-dimensional photochemical model of Titan's atmosphere to estimate the formation rate of precursors macromolecules. We find a production zone slightly lower than 200 km altitude with a total production rate of 4 x 10(exp -14) g/ sq cm s and a C/N approx. = 4. These results are compared with experimental data, and to microphysical models requirements. The Cassini/Huygens mission will bring a detailed picture of the haze distribution and properties, that will be a great challenge for our understanding of those chemical processes.

Screening by imaging: scaling up single-DNA-molecule analysis with a novel parabolic VA-TIRF reflector and noise-reduction techniques.

PubMed

van 't Hoff, Marcel; Reuter, Marcel; Dryden, David T F; Oheim, Martin

2009-09-21

Bacteriophage lambda-DNA molecules are frequently used as a scaffold to characterize the action of single proteins unwinding, translocating, digesting or repairing DNA. However, scaling up such single-DNA-molecule experiments under identical conditions to attain statistically relevant sample sizes remains challenging. Additionally the movies obtained are frequently noisy and difficult to analyse with any precision. We address these two problems here using, firstly, a novel variable-angle total internal reflection fluorescence (VA-TIRF) reflector composed of a minimal set of optical reflective elements, and secondly, using single value decomposition (SVD) to improve the signal-to-noise ratio prior to analysing time-lapse image stacks. As an example, we visualize under identical optical conditions hundreds of surface-tethered single lambda-DNA molecules, stained with the intercalating dye YOYO-1 iodide, and stretched out in a microcapillary flow. Another novelty of our approach is that we arrange on a mechanically driven stage several capillaries containing saline, calibration buffer and lambda-DNA, respectively, thus extending the approach to high-content, high-throughput screening of single molecules. Our length measurements of individual DNA molecules from noise-reduced kymograph images using SVD display a 6-fold enhanced precision compared to raw-data analysis, reaching approximately 1 kbp resolution. Combining these two methods, our approach provides a straightforward yet powerful way of collecting statistically relevant amounts of data in a semi-automated manner. We believe that our conceptually simple technique should be of interest for a broader range of single-molecule studies, well beyond the specific example of lambda-DNA shown here.

Directed Chemical Evolution with an Outsized Genetic Code

PubMed Central

Krusemark, Casey J.; Tilmans, Nicolas P.; Brown, Patrick O.; Harbury, Pehr B.

2016-01-01

The first demonstration that macromolecules could be evolved in a test tube was reported twenty-five years ago. That breakthrough meant that billions of years of chance discovery and refinement could be compressed into a few weeks, and provided a powerful tool that now dominates all aspects of protein engineering. A challenge has been to extend this scientific advance into synthetic chemical space: to enable the directed evolution of abiotic molecules. The problem has been tackled in many ways. These include expanding the natural genetic code to include unnatural amino acids, engineering polyketide and polypeptide synthases to produce novel products, and tagging combinatorial chemistry libraries with DNA. Importantly, there is still no small-molecule analog of directed protein evolution, i.e. a substantiated approach for optimizing complex (≥ 10^9 diversity) populations of synthetic small molecules over successive generations. We present a key advance towards this goal: a tool for genetically-programmed synthesis of small-molecule libraries from large chemical alphabets. The approach accommodates alphabets that are one to two orders of magnitude larger than any in Nature, and facilitates evolution within the chemical spaces they create. This is critical for small molecules, which are built up from numerous and highly varied chemical fragments. We report a proof-of-concept chemical evolution experiment utilizing an outsized genetic code, and demonstrate that fitness traits can be passed from an initial small-molecule population through to the great-grandchildren of that population. The results establish the practical feasibility of engineering synthetic small molecules through accelerated evolution. PMID:27508294

Proton magnetic resonance imaging with para-hydrogen induced polarization.

PubMed

Dechent, Jan F; Buljubasich, Lisandro; Schreiber, Laura M; Spiess, Hans W; Münnemann, Kerstin

2012-02-21

A major challenge in imaging is the detection of small amounts of molecules of interest. In the case of magnetic resonance imaging (MRI) their signals are typically concealed by the large background signal of e.g. the body. This problem can be tackled by hyperpolarization which increases the NMR signals up to several orders of magnitude. However, this strategy is limited for (1)H, the most widely used nucleus in NMR and MRI, because the enormous number of protons in the body screens the small amount of hyperpolarized ones. Here, we describe a method giving rise to high (1)H MRI contrast for hyperpolarized molecules against a large background signal. The contrast is based on the J-coupling induced rephasing of the NMR signal of molecules hyperpolarized via PHIP and it can easily be implemented in common pulse sequences. We discuss several scenarios with different or equal dephasing times T(2)* for the hyperpolarized and thermally polarized compounds and verify our approach by experiments. This method may open up unprecedented opportunities to use the standard MRI nucleus (1)H for e.g. metabolic imaging in the future.

Small-Molecule Binding Aptamers: Selection Strategies, Characterization, and Applications

PubMed Central

Ruscito, Annamaria; DeRosa, Maria C.

2016-01-01

Aptamers are single-stranded, synthetic oligonucleotides that fold into 3-dimensional shapes capable of binding non-covalently with high affinity and specificity to a target molecule. They are generated via an in vitro process known as the Systematic Evolution of Ligands by EXponential enrichment, from which candidates are screened and characterized, and then used in various applications. These applications range from therapeutic uses to biosensors for target detection. Aptamers for small molecule targets such as toxins, antibiotics, molecular markers, drugs, and heavy metals will be the focus of this review. Their accurate detection is needed for the protection and wellbeing of humans and animals. However, the small molecular weights of these targets, including the drastic size difference between the target and the oligonucleotides, make it challenging to select, characterize, and apply aptamers for their detection. Thus, recent (since 2012) notable advances in small molecule aptamers, which have overcome some of these challenges, are presented here, while defining challenges that still exist are discussed. PMID:27242994

Making Mass Spectrometry See the Light: The Promises and Challenges of Cryogenic Infrared Ion Spectroscopy as a Bioanalytical Technique

PubMed Central

Cismesia, Adam P.; Bailey, Laura S.; Bell, Matthew R.; Tesler, Larry F.; Polfer, Nicolas C.

2016-01-01

The detailed chemical information contained in the vibrational spectrum of a cryogenically cooled analyte would, in principle, make infrared (IR) ion spectroscopy a gold standard technique for molecular identification in mass spectrometry. Despite this immense potential, there are considerable challenges in both instrumentation and methodology to overcome before the technique is analytically useful. Here, we discuss the promise of IR ion spectroscopy for small molecule analysis in the context of metabolite identification. Experimental strategies to address sensitivity constraints, poor overall duty cycle, and speed of the experiment are intimately tied to the development of a mass-selective cryogenic trap. Therefore, the most likely avenues for success, in the authors? opinion, are presented here, alongside alternative approaches and some thoughts on data interpretation. PMID:26975370

Multispot single-molecule FRET: High-throughput analysis of freely diffusing molecules

PubMed Central

Panzeri, Francesco

2017-01-01

We describe an 8-spot confocal setup for high-throughput smFRET assays and illustrate its performance with two characteristic experiments. First, measurements on a series of freely diffusing doubly-labeled dsDNA samples allow us to demonstrate that data acquired in multiple spots in parallel can be properly corrected and result in measured sample characteristics consistent with those obtained with a standard single-spot setup. We then take advantage of the higher throughput provided by parallel acquisition to address an outstanding question about the kinetics of the initial steps of bacterial RNA transcription. Our real-time kinetic analysis of promoter escape by bacterial RNA polymerase confirms results obtained by a more indirect route, shedding additional light on the initial steps of transcription. Finally, we discuss the advantages of our multispot setup, while pointing potential limitations of the current single laser excitation design, as well as analysis challenges and their solutions. PMID:28419142

pyQms enables universal and accurate quantification of mass spectrometry data.

PubMed

Leufken, Johannes; Niehues, Anna; Sarin, L Peter; Wessel, Florian; Hippler, Michael; Leidel, Sebastian A; Fufezan, Christian

2017-10-01

Quantitative mass spectrometry (MS) is a key technique in many research areas (1), including proteomics, metabolomics, glycomics, and lipidomics. Because all of the corresponding molecules can be described by chemical formulas, universal quantification tools are highly desirable. Here, we present pyQms, an open-source software for accurate quantification of all types of molecules measurable by MS. pyQms uses isotope pattern matching that offers an accurate quality assessment of all quantifications and the ability to directly incorporate mass spectrometer accuracy. pyQms is, due to its universal design, applicable to every research field, labeling strategy, and acquisition technique. This opens ultimate flexibility for researchers to design experiments employing innovative and hitherto unexplored labeling strategies. Importantly, pyQms performs very well to accurately quantify partially labeled proteomes in large scale and high throughput, the most challenging task for a quantification algorithm. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

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.

Challenges for single molecule electronic devices with nanographene and organic molecules. Do single molecules offer potential as elements of electronic devices in the next generation?

NASA Astrophysics Data System (ADS)

Enoki, Toshiaki; Kiguchi, Manabu

2018-03-01

Interest in utilizing organic molecules to fabricate electronic materials has existed ever since organic (molecular) semiconductors were first discovered in the 1950s. Since then, scientists have devoted serious effort to the creation of various molecule-based electronic systems, such as molecular metals and molecular superconductors. Single-molecule electronics and the associated basic science have emerged over the past two decades and provided hope for the development of highly integrated molecule-based electronic devices in the future (after the Si-based technology era has ended). Here, nanographenes (nano-sized graphene) with atomically precise structures are among the most promising molecules that can be utilized for electronic/spintronic devices. To manipulate single small molecules for an electronic device, a single molecular junction has been developed. It is a powerful tool that allows even small molecules to be utilized. External electric, magnetic, chemical, and mechanical perturbations can change the physical and chemical properties of molecules in a way that is different from bulk materials. Therefore, the various functionalities of molecules, along with changes induced by external perturbations, allows us to create electronic devices that we cannot create using current top-down Si-based technology. Future challenges that involve the incorporation of condensed matter physics, quantum chemistry calculations, organic synthetic chemistry, and electronic device engineering are expected to open a new era in single-molecule device electronic technology.

American Association of Pharmaceutical Scientists National Biotechnology Conference Short Course: Translational Challenges in Developing Antibody-Drug Conjugates: May 24, 2012, San Diego, CA.

PubMed

Thudium, Karen; Bilic, Sanela; Leipold, Douglas; Mallet, William; Kaur, Surinder; Meibohm, Bernd; Erickson, Hans; Tibbitts, Jay; Zhao, Hong; Gupta, Manish

2013-01-01

The American Association of Pharmaceutical Scientists (AAPS) National Biotechnology Conference Short Course "Translational Challenges in Developing Antibody-Drug Conjugates (ADCs)," held May 24, 2012 in San Diego, CA, was organized by members of the Pharmacokinetics, Pharmacodynamics and Drug Metabolism section of AAPS. Representatives from the pharmaceutical industry, regulatory authorities, and academia in the US and Europe attended this short course to discuss the translational challenges in ADC development and the importance of characterizing these molecules early in development to achieve therapeutic utility in patients. Other areas of discussion included selection of target antigens; characterization of absorption, distribution, metabolism, and excretion; assay development and hot topics like regulatory perspectives and the role of pharmacometrics in ADC development. MUC16-targeted ADCs were discussed to illustrate challenges in preclinical development; experiences with trastuzumab emtansine (T-DM1; Genentech) and the recently approved brentuximab vedotin (Adcetris; Seattle Genetics) were presented in depth to demonstrate considerations in clinical development. The views expressed in this report are those of the participants and do not necessarily represent those of their affiliations.

Single molecule data under scrutiny. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb & S.K. Sarkar

NASA Astrophysics Data System (ADS)

Wohland, Thorsten

2015-06-01

Single Molecule Detection and Spectroscopy have grown from their first beginnings into mainstream, mature research areas that are widely applied in the biological sciences. However, despite the advances in technology and the application of many single molecule techniques even in in vivo settings, the data analysis of single molecule experiments is complicated by noise, systematic errors, and complex underlying processes that are only incompletely understood. Colomb and Sarkar provide in this issue an overview of single molecule experiments and the accompanying problems in data analysis, which have to be overcome for a proper interpretation of the experiments [1].

Modeling super-resolution SERS using a T-matrix method to elucidate molecule-nanoparticle coupling and the origins of localization errors

NASA Astrophysics Data System (ADS)

Heaps, Charles W.; Schatz, George C.

2017-06-01

A computational method to model diffraction-limited images from super-resolution surface-enhanced Raman scattering microscopy is introduced. Despite significant experimental progress in plasmon-based super-resolution imaging, theoretical predictions of the diffraction limited images remain a challenge. The method is used to calculate localization errors and image intensities for a single spherical gold nanoparticle-molecule system. The light scattering is calculated using a modification of generalized Mie (T-matrix) theory with a point dipole source and diffraction limited images are calculated using vectorial diffraction theory. The calculation produces the multipole expansion for each emitter and the coherent superposition of all fields. Imaging the constituent fields in addition to the total field provides new insight into the strong coupling between the molecule and the nanoparticle. Regardless of whether the molecular dipole moment is oriented parallel or perpendicular to the nanoparticle surface, the anisotropic excitation distorts the center of the nanoparticle as measured by the point spread function by approximately fifty percent of the particle radius toward to the molecule. Inspection of the nanoparticle multipoles reveals that distortion arises from a weak quadrupole resonance interfering with the dipole field in the nanoparticle. When the nanoparticle-molecule fields are in-phase, the distorted nanoparticle field dominates the observed image. When out-of-phase, the nanoparticle and molecule are of comparable intensity and interference between the two emitters dominates the observed image. The method is also applied to different wavelengths and particle radii. At off-resonant wavelengths, the method predicts images closer to the molecule not because of relative intensities but because of greater distortion in the nanoparticle. The method is a promising approach to improving the understanding of plasmon-enhanced super-resolution experiments.

CRISPR Approaches to Small Molecule Target Identification. | Office of Cancer Genomics

Cancer.gov

A long-standing challenge in drug development is the identification of the mechanisms of action of small molecules with therapeutic potential. A number of methods have been developed to address this challenge, each with inherent strengths and limitations. We here provide a brief review of these methods with a focus on chemical-genetic methods that are based on systematically profiling the effects of genetic perturbations on drug sensitivity.

Bronchial biopsy evidence for leukocyte infiltration and upregulation of leukocyte-endothelial cell adhesion molecules 6 hours after local allergen challenge of sensitized asthmatic airways.

PubMed Central

Montefort, S; Gratziou, C; Goulding, D; Polosa, R; Haskard, D O; Howarth, P H; Holgate, S T; Carroll, M P

1994-01-01

We have examined the mucosal changes occurring in bronchial biopsies from six atopic asthmatics 5-6 h after local endobronchial allergen challenge and compared them with biopsies from saline-challenged segments from the same subjects at the same time point. All the subjects developed localized bronchoconstriction in the allergen-challenged segment and had a decrease in forced expiratory volume in 1 s (FEV1) (P < 0.01) and a decrease in their methacholine provocative concentration of agonist required to reduce FEV1 from baseline by 20% (P < 0.05) 24 h postchallenge. At 6 h we observed an increase in neutrophils (P = 0.03), eosinophils (P = 0.025), mast cells (P = 0.03), and CD3+ lymphocytes (P = 0.025), but not in CD4+ or CD8+ lymphocyte counts. We also detected an increase in endothelial intercellular adhesion molecule type 1 (P < 0.05) and E-selectin (P < 0.005), but not vascular cell adhesion molecule type 1 expression with a correlative increase in submucosal and epithelial LFA+ leucocytes (P < 0.01). Thus, in sensitized asthmatics, local endobronchial allergen instillation leads to an increased inflammatory cell infiltrate of the airway mucosa that involves upregulation of specific adhesion molecules expressed on the microvasculature. Images PMID:7512980

Contactless experiments on individual DNA molecules show no evidence for molecular wire behavior.

PubMed

Gómez-Navarro, C; Moreno-Herrero, F; de Pablo, P J; Colchero, J; Gómez-Herrero, J; Baró, A M

2002-06-25

A fundamental requirement for a molecule to be considered a molecular wire (MW) is the ability to transport electrical charge with a reasonably low resistance. We have carried out two experiments that measure first, the charge transfer from an electrode to the molecule, and second, the dielectric response of the MW. The latter experiment requires no contacts to either end of the molecule. From our experiments we conclude that adsorbed individual DNA molecules have a resistivity similar to mica, glass, and silicon oxide substrates. Therefore adsorbed DNA is not a conductor, and it should not be considered as a viable candidate for MW applications. Parallel studies on other nanowires, including single-walled carbon nanotubes, showed conductivity as expected.

Evolution of organic molecules under Mars-like UV radiation conditions in space and laboratory

NASA Astrophysics Data System (ADS)

Rouquette, L.; Stalport, F.; Cottin, H.; Coll, P.; Szopa, C.; Saiagh, K.; Poch, O.; Khalaf, D.; Chaput, D.; Grira, K.; Dequaire, T.

2017-09-01

The detection and identification of organic molecules at Mars are of prime importance, as some of these molecules are life precursors and components. While in situ planetary missions are searching for them, it is essential to understand how organic molecules evolve and are preserved at the surface of Mars. Indeed the harsh conditions of the environment of Mars such as ultraviolet (UV) radiation or oxidative processes could explain the low abundance and diversity of organic molecules detected by now [1]. In order to get a better understanding of the evolution of organic matter at the surface of Mars, we exposed organic molecules under a Mars-like UV radiation environment. Similar organic samples were exposed to the Sun radiation, outside the International Space Station (ISS), and under a UV lamp (martian pressure and temperature conditions) in the laboratory. In both experiments, organic molecules tend to photodegrade under Mars-like UV radiation. Minerals, depending on their nature, can protect or accelerate the degradation of organic molecules. For some molecules, new products, possibly photoresistant, seem to be produced. Finally, experimenting in space allow us to get close to in situ conditions and to validate our laboratory experiment while the laboratory experiment is essential to study the evolution of a large amount and diversity of organic molecules.

Directly measuring single-molecule heterogeneity using force spectroscopy

PubMed Central

Hinczewski, Michael; Thirumalai, D.

2016-01-01

One of the most intriguing results of single-molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active conformations. The structural differences between these conformations may be subtle, but each distinct state can be remarkably long-lived, with interconversions between states occurring only at macroscopic timescales, fractions of a second or longer. Although we now have proof of functional heterogeneity in a handful of systems—enzymes, motors, adhesion complexes—identifying and measuring it remains a formidable challenge. Here, we show that evidence of this phenomenon is more widespread than previously known, encoded in data collected from some of the most well-established single-molecule techniques: atomic force microscopy or optical tweezer pulling experiments. We present a theoretical procedure for analyzing distributions of rupture/unfolding forces recorded at different pulling speeds. This results in a single parameter, quantifying the degree of heterogeneity, and also leads to bounds on the equilibration and conformational interconversion timescales. Surveying 10 published datasets, we find heterogeneity in 5 of them, all with interconversion rates slower than 10 s−1. Moreover, we identify two systems where additional data at realizable pulling velocities is likely to find a theoretically predicted, but so far unobserved crossover regime between heterogeneous and nonheterogeneous behavior. The significance of this regime is that it will allow far more precise estimates of the slow conformational switching times, one of the least understood aspects of functional heterogeneity. PMID:27317744

Fluid flow enhances the effectiveness of toxin export by aquatic microorganisms: a first-passage perspective

NASA Astrophysics Data System (ADS)

Licata, Nicholas; Clark, Aaron

2014-03-01

Aquatic microorganisms face a variety of challenges in the course of development. One central challenge is efficiently regulating the export of toxic molecules inside the developing embryo. The strategies employed should be robust with respect to the variable ocean environment and limit the chances that exported toxins are reabsorbed. In this talk we consider the first-passage problem for the uptake of exported toxins by a spherical embryo. A perturbative solution of the advection-diffusion equation reveals that a concentration boundary layer forms in the vicinity of the embryo, and that fluid flow enhances the effectiveness of toxin export. We highlight connections between the model results and recent experiments on the development of sea urchin embryos. We acknowledge financial support from the University of Michigan-Dearobrn CASL Faculty Summer Research Grant.

The Origin of Primitive Cells, Nutrient Intake, and Non-Enzymatic Elongation of Encapsulated Nucleotides

NASA Technical Reports Server (NTRS)

Meierhenrich, Uwe J.; Filippi, Jean-Jacques; Meinert, Cornelia; Vierling, Pierre; Dworkin, Jason P.

2009-01-01

Fatty acids and fatty alcohols are commonly found in experiments simulating the prebiotic 'soup'. These amphiphiles can be synthesized under prebiotic conditions, at least as long as the molecules are chemically relatively simple and do not need to be enantiomerically pure. In the context of topical origin-of-life theories, two distinct formation pathways for amphiphiles have been described; one related to geophysical sites, such as marine hydrothermal systems, and another to extraterrestrial sources, such as the proto-solar nebula, which was fed by interplanetary and interstellar nebulae. The chemical analysis of each provides individual characteristic challenges.

Vacancy effects on the electronic and structural properties pentacene

NASA Astrophysics Data System (ADS)

Laraib, Iflah; Janotti, Anderson

Defects in organic crystals are likely to affect charge transport in organic electronic devices. Vacancies can create lattice distortions and modify electronic states associated with the molecules in its surrounding. Spectroscopy experiments indicate that molecular vacancies trap charge carriers. Experimental characterization of individual defects is challenging and unambiguous. Here we use density functional calculations including van der Waals interactions in a supercell approach to study the single vacancy in pentacene, a prototype organic semiconductor. We determine formation energies, local lattice relaxations, and discuss how vacancies locally distort the lattice and affect the electronic properties of the host organic semiconductor.

Fast live cell imaging at nanometer scale using annihilating filter-based low-rank Hankel matrix approach

NASA Astrophysics Data System (ADS)

Min, Junhong; Carlini, Lina; Unser, Michael; Manley, Suliana; Ye, Jong Chul

2015-09-01

Localization microscopy such as STORM/PALM can achieve a nanometer scale spatial resolution by iteratively localizing fluorescence molecules. It was shown that imaging of densely activated molecules can accelerate temporal resolution which was considered as major limitation of localization microscopy. However, this higher density imaging needs to incorporate advanced localization algorithms to deal with overlapping point spread functions (PSFs). In order to address this technical challenges, previously we developed a localization algorithm called FALCON1, 2 using a quasi-continuous localization model with sparsity prior on image space. It was demonstrated in both 2D/3D live cell imaging. However, it has several disadvantages to be further improved. Here, we proposed a new localization algorithm using annihilating filter-based low rank Hankel structured matrix approach (ALOHA). According to ALOHA principle, sparsity in image domain implies the existence of rank-deficient Hankel structured matrix in Fourier space. Thanks to this fundamental duality, our new algorithm can perform data-adaptive PSF estimation and deconvolution of Fourier spectrum, followed by truly grid-free localization using spectral estimation technique. Furthermore, all these optimizations are conducted on Fourier space only. We validated the performance of the new method with numerical experiments and live cell imaging experiment. The results confirmed that it has the higher localization performances in both experiments in terms of accuracy and detection rate.

Liquid xenon purification, de-radonation (and de-kryptonation)

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

Pocar, Andrea, E-mail: pocar@umass.edu; Physics Division, Lawrence Livermore National Laboratory, Livermore, California 94550

Liquid xenon detectors are at the forefront of rare event physics, including searches for neutrino-less double beta decay and WIMP dark matter. The xenon for these experiments needs to be purified from chemical impurities such as electronegative atoms and molecules, which absorb ionization electrons, and VUV (178 nm) scintillation light-absorbing chemical species. In addition, superb purification from radioactive impurities is required. Particularly challenging are radioactive noble isotopes ({sup 85}Kr,{sup 39,42}Ar,{sup 220,222}Rn). Radon is a particularly universal problem, due to the extended decay sequence of its daughters and its ubiquitous presence in detector materials. Purification and de-radonation of liquid xenon aremore » addressed with particular focus on the experience gained with the EXO-200 neutrino-less double beta decay detector.« less

Quantum Monte Carlo Calculations Applied to Magnetic Molecules

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

Engelhardt, Larry

2006-01-01

We have calculated the equilibrium thermodynamic properties of Heisenberg spin systems using a quantum Monte Carlo (QMC) method. We have used some of these systems as models to describe recently synthesized magnetic molecules, and-upon comparing the results of these calculations with experimental data-have obtained accurate estimates for the basic parameters of these models. We have also performed calculations for other systems that are of more general interest, being relevant both for existing experimental data and for future experiments. Utilizing the concept of importance sampling, these calculations can be carried out in an arbitrarily large quantum Hilbert space, while still avoidingmore » any approximations that would introduce systematic errors. The only errors are statistical in nature, and as such, their magnitudes are accurately estimated during the course of a simulation. Frustrated spin systems present a major challenge to the QMC method, nevertheless, in many instances progress can be made. In this chapter, the field of magnetic molecules is introduced, paying particular attention to the characteristics that distinguish magnetic molecules from other systems that are studied in condensed matter physics. We briefly outline the typical path by which we learn about magnetic molecules, which requires a close relationship between experiments and theoretical calculations. The typical experiments are introduced here, while the theoretical methods are discussed in the next chapter. Each of these theoretical methods has a considerable limitation, also described in Chapter 2, which together serve to motivate the present work. As is shown throughout the later chapters, the present QMC method is often able to provide useful information where other methods fail. In Chapter 3, the use of Monte Carlo methods in statistical physics is reviewed, building up the fundamental ideas that are necessary in order to understand the method that has been used in this work. With these ideas in hand, we then provide a detailed explanation of the current QMC method in Chapter 4. The remainder of the thesis is devoted to presenting specific results: Chapters 5 and 6 contain articles in which this method has been used to answer general questions that are relevant to broad classes of systems. Then, in Chapter 7, we provide an analysis of four different species of magnetic molecules that have recently been synthesized and studied. In all cases, comparisons between QMC calculations and experimental data allow us to distinguish a viable microscopic model and make predictions for future experiments. In Chapter 8, the infamous ''negative sign problem'' is described in detail, and we clearly indicate the limitations on QMC that are imposed by this obstacle. Finally, Chapter 9 contains a summary of the present work and the expected directions for future research.« less

Diagnostic Applications of Next Generation Sequencing in Immunogenetics and Molecular Oncology

PubMed Central

Grumbt, Barbara; Eck, Sebastian H.; Hinrichsen, Tanja; Hirv, Kaimo

2013-01-01

Summary With the introduction of the next generation sequencing (NGS) technologies, remarkable new diagnostic applications have been established in daily routine. Implementation of NGS is challenging in clinical diagnostics, but definite advantages and new diagnostic possibilities make the switch to the technology inevitable. In addition to the higher sequencing capacity, clonal sequencing of single molecules, multiplexing of samples, higher diagnostic sensitivity, workflow miniaturization, and cost benefits are some of the valuable features of the technology. After the recent advances, NGS emerged as a proven alternative for classical Sanger sequencing in the typing of human leukocyte antigens (HLA). By virtue of the clonal amplification of single DNA molecules ambiguous typing results can be avoided. Simultaneously, a higher sample throughput can be achieved by tagging of DNA molecules with multiplex identifiers and pooling of PCR products before sequencing. In our experience, up to 380 samples can be typed for HLA-A, -B, and -DRB1 in high-resolution during every sequencing run. In molecular oncology, NGS shows a markedly increased sensitivity in comparison to the conventional Sanger sequencing and is developing to the standard diagnostic tool in detection of somatic mutations in cancer cells with great impact on personalized treatment of patients. PMID:23922545

Molecular dynamics simulation, ab initio calculation, and size-selected anion photoelectron spectroscopy study of initial hydration processes of calcium chloride.

PubMed

He, Zhili; Feng, Gang; Yang, Bin; Yang, Lijiang; Liu, Cheng-Wen; Xu, Hong-Guang; Xu, Xi-Ling; Zheng, Wei-Jun; Gao, Yi Qin

2018-06-14

To understand the initial hydration processes of CaCl 2 , we performed molecular simulations employing the force field based on the theory of electronic continuum correction with rescaling. Integrated tempering sampling molecular dynamics were combined with ab initio calculations to overcome the sampling challenge in cluster structure search and refinement. The calculated vertical detachment energies of CaCl 2 (H 2 O) n - (n = 0-8) were compared with the values obtained from photoelectron spectra, and consistency was found between the experiment and computation. Separation of the Cl-Ca ion pair is investigated in CaCl 2 (H 2 O) n - anions, where the first Ca-Cl ionic bond required 4 water molecules, and both Ca-Cl bonds are broken when the number of water molecules is larger than 7. For neutral CaCl 2 (H 2 O) n clusters, breaking of the first Ca-Cl bond starts at n = 5, and 8 water molecules are not enough to separate the two ion pairs. Comparing with the observations on magnesium chloride, it shows that separating one ion pair in CaCl 2 (H 2 O) n requires fewer water molecules than those for MgCl 2 (H 2 O) n . Coincidentally, the solubility of calcium chloride is higher than that of magnesium chloride in bulk solutions.

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.

Molecular dynamics simulation, ab initio calculation, and size-selected anion photoelectron spectroscopy study of initial hydration processes of calcium chloride

NASA Astrophysics Data System (ADS)

He, Zhili; Feng, Gang; Yang, Bin; Yang, Lijiang; Liu, Cheng-Wen; Xu, Hong-Guang; Xu, Xi-Ling; Zheng, Wei-Jun; Gao, Yi Qin

2018-06-01

To understand the initial hydration processes of CaCl2, we performed molecular simulations employing the force field based on the theory of electronic continuum correction with rescaling. Integrated tempering sampling molecular dynamics were combined with ab initio calculations to overcome the sampling challenge in cluster structure search and refinement. The calculated vertical detachment energies of CaCl2(H2O)n- (n = 0-8) were compared with the values obtained from photoelectron spectra, and consistency was found between the experiment and computation. Separation of the Cl—Ca ion pair is investigated in CaCl2(H2O)n- anions, where the first Ca—Cl ionic bond required 4 water molecules, and both Ca—Cl bonds are broken when the number of water molecules is larger than 7. For neutral CaCl2(H2O)n clusters, breaking of the first Ca—Cl bond starts at n = 5, and 8 water molecules are not enough to separate the two ion pairs. Comparing with the observations on magnesium chloride, it shows that separating one ion pair in CaCl2(H2O)n requires fewer water molecules than those for MgCl2(H2O)n. Coincidentally, the solubility of calcium chloride is higher than that of magnesium chloride in bulk solutions.

Biosimilars--global issues, national solutions.

PubMed

Knezevic, Ivana; Griffiths, Elwyn

2011-09-01

Biotechnology derived medicinal products are presently the best characterized biologicals with considerable production and clinical experience, and have revolutionized the treatment of some of the most difficult-to-treat diseases, prolonging and improving the quality of life and patient care. They are also currently one of the fastest growing segments of the pharmaceutical industry market. The critical challenge that the biopharmaceutical industry is facing is the expiry of patents for the first generation of biopharmaceuticals, mainly recombinant DNA derived products, such as interferons, growth hormone and erythropoetin. The question that immediately arose was how should such copies of the originator products be licensed, bearing in mind that they are highly complex biological molecules produced by equally complex biological production processes with their inherent problem of biological variability. Copying biologicals is much more complex than copying small molecules and the critical issue was how to handle the licensing of products if relying in part on data from an innovator product. Since 2004 there has been considerable international consultation on how to deal with biosimilars and biological copy products. This has led to a better understanding of the challenges in the regulatory evaluation of the quality, safety and efficacy of "biosimilars", to the exchange of information between regulators, as well as to the identification of key issues. The aim of this article is to provide a brief overview of the scientific and regulatory challenges faced in developing and evaluating similar biotherapeutic products for global use. It is intended as an introduction to the series of articles in this special issue of Biologicals devoted to similar biotherapeutic products. Copyright © 2011. Published by Elsevier Ltd.

CAR T-cell immunotherapy: The path from the by-road to the freeway?

PubMed

Whilding, Lynsey M; Maher, John

2015-12-01

Chimeric antigen receptors are genetically encoded artificial fusion molecules that can re-program the specificity of peripheral blood polyclonal T-cells against a selected cell surface target. Unparallelled clinical efficacy has recently been demonstrated using this approach to treat patients with refractory B-cell malignancy. However, the approach is technically challenging and can elicit severe toxicity in patients. Moreover, solid tumours have largely proven refractory to this approach. In this review, we describe the important structural features of CARs and how this may influence function. Emerging clinical experience is summarized in both solid tumours and haematological malignancies. Finally, we consider the particular challenges imposed by solid tumours to the successful development of CAR T-cell immunotherapy, together with a number of innovative strategies that have been developed in an effort to reverse the balance in favour of therapeutic benefit. Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.

50th Anniversary Perspective: A Perspective on Polyelectrolyte Solutions

PubMed Central

2017-01-01

From the beginning of life with the information-containing polymers until the present era of a plethora of water-based materials in health care industry and biotechnology, polyelectrolytes are ubiquitous with a broad range of structural and functional properties. The main attribute of polyelectrolyte solutions is that all molecules are strongly correlated both topologically and electrostatically in their neutralizing background of charged ions in highly polarizable solvent. These strong correlations and the necessary use of numerous variables in experiments on polyelectrolytes have presented immense challenges toward fundamental understanding of the various behaviors of charged polymeric systems. This Perspective presents the author’s subjective summary of several conceptual advances and the remaining persistent challenges in the contexts of charge and size of polymers, structures in homogeneous solutions, thermodynamic instability and phase transitions, structural evolution with oppositely charged polymers, dynamics in polyelectrolyte solutions, kinetics of phase separation, mobility of charged macromolecules between compartments, and implications to biological systems. PMID:29296029

Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays.

PubMed

Mak, Angel C Y; Lai, Yvonne Y Y; Lam, Ernest T; Kwok, Tsz-Piu; Leung, Alden K Y; Poon, Annie; Mostovoy, Yulia; Hastie, Alex R; Stedman, William; Anantharaman, Thomas; Andrews, Warren; Zhou, Xiang; Pang, Andy W C; Dai, Heng; Chu, Catherine; Lin, Chin; Wu, Jacob J K; Li, Catherine M L; Li, Jing-Woei; Yim, Aldrin K Y; Chan, Saki; Sibert, Justin; Džakula, Željko; Cao, Han; Yiu, Siu-Ming; Chan, Ting-Fung; Yip, Kevin Y; Xiao, Ming; Kwok, Pui-Yan

2016-01-01

Comprehensive whole-genome structural variation detection is challenging with current approaches. With diploid cells as DNA source and the presence of numerous repetitive elements, short-read DNA sequencing cannot be used to detect structural variation efficiently. In this report, we show that genome mapping with long, fluorescently labeled DNA molecules imaged on nanochannel arrays can be used for whole-genome structural variation detection without sequencing. While whole-genome haplotyping is not achieved, local phasing (across >150-kb regions) is routine, as molecules from the parental chromosomes are examined separately. In one experiment, we generated genome maps from a trio from the 1000 Genomes Project, compared the maps against that derived from the reference human genome, and identified structural variations that are >5 kb in size. We find that these individuals have many more structural variants than those published, including some with the potential of disrupting gene function or regulation. Copyright © 2016 by the Genetics Society of America.

Robust model-based analysis of single-particle tracking experiments with Spot-On

PubMed Central

Grimm, Jonathan B; Lavis, Luke D

2018-01-01

Single-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding and diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due to biases in both data analysis and experimental design. To address analysis bias, we introduce ‘Spot-On’, an intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving out-of-focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule trajectories. To minimize inherent experimental biases, we implement and validate stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and tracking errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On outperforms other methods. We then apply Spot-On to spaSPT data from live mammalian cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently and robustly infers subpopulation fractions and diffusion constants. PMID:29300163

Robust model-based analysis of single-particle tracking experiments with Spot-On.

PubMed

Hansen, Anders S; Woringer, Maxime; Grimm, Jonathan B; Lavis, Luke D; Tjian, Robert; Darzacq, Xavier

2018-01-04

Single-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding and diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due to biases in both data analysis and experimental design. To address analysis bias, we introduce 'Spot-On', an intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving out-of-focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule trajectories. To minimize inherent experimental biases, we implement and validate stroboscopic photo-activation SPT (spaSPT), which minimizes motion-blur bias and tracking errors. We validate Spot-On using experimentally realistic simulations and show that Spot-On outperforms other methods. We then apply Spot-On to spaSPT data from live mammalian cells spanning a wide range of nuclear dynamics and demonstrate that Spot-On consistently and robustly infers subpopulation fractions and diffusion constants. © 2018, Hansen et al.

Interfacial self-assembled functional nanoparticle array: a facile surface-enhanced Raman scattering sensor for specific detection of trace analytes.

PubMed

Zhang, Kun; Ji, Ji; Li, Yixin; Liu, Baohong

2014-07-01

Surface-enhanced Raman scattering (SERS) has proven to be promising for the detection of trace analytes; however, the precise nanofabrication of a specific and sensitive plasmonic SERS-active substrate is still a major challenge that limits the scope of its applications. In this work, gold nanoparticles are self-assembled into densely packed two-dimensional arrays at a liquid/liquid interface between dimethyl carbonate and water in the absence of template controller molecules. Both the simulation and experiment results show that the particles within these film-like arrays exhibit strong electromagnetic coupling and enable large amplification of Raman signals. In order to realize the level of sensing specificity, the surface chemistry of gold nanoparticles (Au NPs) is rationally tailored by incorporating an appropriate chemical moiety that specifically captures molecules of interest. The ease of fabrication and good uniformity make this platform ideal for in situ SERS sensing of trace targets in complex samples.

An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.

PubMed

Keedy, Daniel A; Hill, Zachary B; Biel, Justin T; Kang, Emily; Rettenmaier, T Justin; Brandao-Neto, Jose; Pearce, Nicholas M; von Delft, Frank; Wells, James A; Fraser, James S

2018-06-07

Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here we have identified allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands. Our results converge on allosteric sites that are conformationally coupled to the active-site WPD loop and are hotspots for fragment binding. Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure, revealed here by multitemperature crystallography, can elucidate allosteric mechanisms and open new doors for long-range control of protein function. © 2018, Keedy et al.

Engineering the magnetic coupling and anisotropy at the molecule–magnetic surface interface in molecular spintronic devices

PubMed Central

Campbell, Victoria E.; Tonelli, Monica; Cimatti, Irene; Moussy, Jean-Baptiste; Tortech, Ludovic; Dappe, Yannick J.; Rivière, Eric; Guillot, Régis; Delprat, Sophie; Mattana, Richard; Seneor, Pierre; Ohresser, Philippe; Choueikani, Fadi; Otero, Edwige; Koprowiak, Florian; Chilkuri, Vijay Gopal; Suaud, Nicolas; Guihéry, Nathalie; Galtayries, Anouk; Miserque, Frederic; Arrio, Marie-Anne; Sainctavit, Philippe; Mallah, Talal

2016-01-01

A challenge in molecular spintronics is to control the magnetic coupling between magnetic molecules and magnetic electrodes to build efficient devices. Here we show that the nature of the magnetic ion of anchored metal complexes highly impacts the exchange coupling of the molecules with magnetic substrates. Surface anchoring alters the magnetic anisotropy of the cobalt(II)-containing complex (Co(Pyipa)2), and results in blocking of its magnetization due to the presence of a magnetic hysteresis loop. In contrast, no hysteresis loop is observed in the isostructural nickel(II)-containing complex (Ni(Pyipa)2). Through XMCD experiments and theoretical calculations we find that Co(Pyipa)2 is strongly ferromagnetically coupled to the surface, while Ni(Pyipa)2 is either not coupled or weakly antiferromagnetically coupled to the substrate. These results highlight the importance of the synergistic effect that the electronic structure of a metal ion and the organic ligands has on the exchange interaction and anisotropy occurring at the molecule–electrode interface. PMID:27929089

On the limited recognition of inorganic surfaces by short peptides compared with antibodies.

PubMed

Artzy-Schnirman, Arbel; Abu-Shah, Enas; Dishon, Matan; Soifer, Hadas; Sivan, Yotam; Reiter, Yoram; Benhar, Itai; Sivan, Uri

2014-06-01

The vast potential applications of biomolecules that bind inorganic surfaces led mostly to the isolation of short peptides that target selectively specific materials. The demonstrated differential affinity toward certain surfaces created the impression that the recognition capacity of short peptides may match that of rigid biomolecules. In the following, we challenge this view by comparing the capacity of antibody molecules to discriminate between the (100) and (111A) facets of a gallium arsenide semiconductor crystal with the capacity of short peptides to do the same. Applying selection from several peptide and single chain phage display libraries, we find a number of antibody molecules that bind preferentially a given crystal facet but fail to isolate, in dozens of attempts, a single peptide capable of such recognition. The experiments underscore the importance of rigidity to the recognition of inorganic flat targets and therefore set limitations on potential applications of short peptides in biomimetics. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.

Nonequilibrium thermodynamics of dilute polymer solutions in flow.

PubMed

Latinwo, Folarin; Hsiao, Kai-Wen; Schroeder, Charles M

2014-11-07

Modern materials processing applications and technologies often occur far from equilibrium. To this end, the processing of complex materials such as polymer melts and nanocomposites generally occurs under strong deformations and flows, conditions under which equilibrium thermodynamics does not apply. As a result, the ability to determine the nonequilibrium thermodynamic properties of polymeric materials from measurable quantities such as heat and work is a major challenge in the field. Here, we use work relations to show that nonequilibrium thermodynamic quantities such as free energy and entropy can be determined for dilute polymer solutions in flow. In this way, we determine the thermodynamic properties of DNA molecules in strong flows using a combination of simulations, kinetic theory, and single molecule experiments. We show that it is possible to calculate polymer relaxation timescales purely from polymer stretching dynamics in flow. We further observe a thermodynamic equivalence between nonequilibrium and equilibrium steady-states for polymeric systems. In this way, our results provide an improved understanding of the energetics of flowing polymer solutions.

Electronic Excitations of Alkali-Alkaline Earth Diatomic Molecules - Results from AB Initio Calculations

NASA Astrophysics Data System (ADS)

Pototschnig, Johann V.; Krois, Günter; Lackner, Florian; Ernst, Wolfgang E.

2014-06-01

Recently interest in polar diatomic molecules with a magnetic dipole moment has been growing. An example for such molecules is the combination of an alkali metal atom and an alkaline earth metal atom. These systems are quite small, containing only three valence electrons. Nevertheless calculations of excited states are challenging. Ab initio calculations for two sample systems, LiCa and RbSr, will be presented. The potential energy curves and transition dipole moments for the ground state and several excited states were determined, up to 25000 wn for LiCa and up to 22000 wn for RbSr. Multireference configuration interaction calculations (MRCI) based on complete active space self-consistent field wave functions (CASSCF) were used to determine the properties of the system as implemented in the MOLPRO software package. Effective core potentials (ECPs) and core polarization potentials (CCPs) were applied to reduce the computational effort, while retaining accuracy. The similarities and differences of the two systems will be discussed. In both systems the accurate description of the asymptotic values of the PECs corresponding to atomic D-states proved to be difficult. The results will be compared to recent experiments, showing that a combination of theory and experiment gives a reliable description of the systems. G. Krois, J.V. Pototschnig, F. Lackner and W.E. Ernst, J. Phys. Chem. A, 117, 13719-13731 (2013) H.-J. Werner and P. J. Knowles and G. Knizia and F. R. Manby and M. {Schütz} et al., MOLPRO, version 2010.1, see http://www.molpro.net/

New strategy for protein interactions and application to structure-based drug design

NASA Astrophysics Data System (ADS)

Zou, Xiaoqin

One of the greatest challenges in computational biophysics is to predict interactions between biological molecules, which play critical roles in biological processes and rational design of therapeutic drugs. Biomolecular interactions involve delicate interplay between multiple interactions, including electrostatic interactions, van der Waals interactions, solvent effect, and conformational entropic effect. Accurate determination of these complex and subtle interactions is challenging. Moreover, a biological molecule such as a protein usually consists of thousands of atoms, and thus occupies a huge conformational space. The large degrees of freedom pose further challenges for accurate prediction of biomolecular interactions. Here, I will present our development of physics-based theory and computational modeling on protein interactions with other molecules. The major strategy is to extract microscopic energetics from the information embedded in the experimentally-determined structures of protein complexes. I will also present applications of the methods to structure-based therapeutic design. Supported by NSF CAREER Award DBI-0953839, NIH R01GM109980, and the American Heart Association (Midwest Affiliate) [13GRNT16990076].

Use of Carboxymethyl-beta-cyclodextrin (CMCD) as Flushing Agent for Remediation of Metal Contaminated Soil

NASA Astrophysics Data System (ADS)

Skold, M. E.; Thyne, G. D.; McCray, J. E.; Drexler, J. W.

2005-12-01

One of the major challenges in remediating soil and ground water is the presence of mixed organic and inorganic contaminants. Due to their very different behavior, research has to a large extent focused on remediation of either organic or inorganic contaminants rather than mixed waste. Cyclodextrins (CDs) are a group of non-toxic sugar based molecules that do not sorb to soil particles and do not experience pore size exclusion. Thus, they have good hydraulic properties. CDs enhance the solubility of organic compounds by forming inclusion complexes between organic contaminants and the non-polar cavity at the center of the CD. By substituting functional groups to the cyclodextrin molecule it can form complexes with heavy metals. Previous studies have shown that carboxymethyl-beta-cyclodextrin (CMCD) can simultaneously complex organic and inorganic contaminants. The aim of this study is to compare how strongly CMCD complexes several common heavy metals, radioactive elements and a common divalent cation. Results from batch experiments show that CMCD has the ability to complex a wide array of heavy metals and radioactive elements. The solubility of metal oxalates and metal oxides clearly increased in the presence of CMCD. Logarithmic conditional formation constants ranged from 3.5 to 6 for heavy metals and from 3 to 6 for radioactive elements. Calcium, which may compete for binding sites, has a logarithmic conditional formation constant of 3.1. Batch experiments performed at 10 and 25 degrees C showed little temperature effect on conditional formation constants. Results from batch experiments were compared to results from column experiments where Pb was sorbed onto hydrous ferric oxide coated sand and subsequently removed by a CMCD solution. The results indicate that CMCD is a potential flushing agent for remediation of mixed waste sites.

In situ temperature monitoring in single-molecule FRET experiments

NASA Astrophysics Data System (ADS)

Hartmann, Andreas; Berndt, Frederic; Ollmann, Simon; Krainer, Georg; Schlierf, Michael

2018-03-01

Thermodynamic properties of single molecules including enthalpic and entropic contributions are often determined from experiments by a direct control and precise measurement of the local temperature. However, common temperature monitoring techniques using, for example, ultrafine temperature probes can lead to uncertainties as the probe cannot be placed in the vicinity of the molecule of interest. Here, we devised an approach to measure the local temperature in freely diffusing confocal single-molecule Förster Resonance Energy Transfer (smFRET) experiments in situ by directly adding the temperature-sensitive fluorescent dye Rhodamine B, whose fluorescence lifetime serves as a probe of the local temperature in the confocal volume. We demonstrate that the temperature and FRET efficiencies of static and dynamic molecules can be extracted within one measurement simultaneously, without the need of a reference chamber. We anticipate this technique to be particularly useful in the physicochemical analyses of temperature-dependent biomolecular processes from single-molecule measurements.

Challenges of curcumin bioavailability: novel aerosol remedies.

PubMed

Subramani, Parasuraman Aiya; Narala, Venkata R

2013-01-01

Nanoparticles are promising aids for drug delivery for previously challenging diseases, and many incurable ones. Curcumin (diferuloylmethane) is a pleiotropic molecule having various target molecules in the body. Despite its effects, curcumin-based drugs are not readily available in the market because of their low bioavailability. Although dietary intake and knowledge about the potential of curcumin are high in countries like India, studies indicate that the bioavailability problem still persists. However, administration of curcumin through inhalation has received little consideration. In this review we discuss the potential of curcumin, approaches made to overcome the bioavailability challenges, and novel approaches that could be applied in order to deliver curcumin in a pressurized metered dose inhaler (pMDI).

A drug-compatible and temperature-controlled microfluidic device for live-cell imaging.

PubMed

Chen, Tong; Gomez-Escoda, Blanca; Munoz-Garcia, Javier; Babic, Julien; Griscom, Laurent; Wu, Pei-Yun Jenny; Coudreuse, Damien

2016-08-01

Monitoring cellular responses to changes in growth conditions and perturbation of targeted pathways is integral to the investigation of biological processes. However, manipulating cells and their environment during live-cell-imaging experiments still represents a major challenge. While the coupling of microfluidics with microscopy has emerged as a powerful solution to this problem, this approach remains severely underexploited. Indeed, most microdevices rely on the polymer polydimethylsiloxane (PDMS), which strongly absorbs a variety of molecules commonly used in cell biology. This effect of the microsystems on the cellular environment hampers our capacity to accurately modulate the composition of the medium and the concentration of specific compounds within the microchips, with implications for the reliability of these experiments. To overcome this critical issue, we developed new PDMS-free microdevices dedicated to live-cell imaging that show no interference with small molecules. They also integrate a module for maintaining precise sample temperature both above and below ambient as well as for rapid temperature shifts. Importantly, changes in medium composition and temperature can be efficiently achieved within the chips while recording cell behaviour by microscopy. Compatible with different model systems, our platforms provide a versatile solution for the dynamic regulation of the cellular environment during live-cell imaging. © 2016 The Authors.

A drug-compatible and temperature-controlled microfluidic device for live-cell imaging

PubMed Central

Chen, Tong; Gomez-Escoda, Blanca; Munoz-Garcia, Javier; Babic, Julien; Griscom, Laurent; Wu, Pei-Yun Jenny

2016-01-01

Monitoring cellular responses to changes in growth conditions and perturbation of targeted pathways is integral to the investigation of biological processes. However, manipulating cells and their environment during live-cell-imaging experiments still represents a major challenge. While the coupling of microfluidics with microscopy has emerged as a powerful solution to this problem, this approach remains severely underexploited. Indeed, most microdevices rely on the polymer polydimethylsiloxane (PDMS), which strongly absorbs a variety of molecules commonly used in cell biology. This effect of the microsystems on the cellular environment hampers our capacity to accurately modulate the composition of the medium and the concentration of specific compounds within the microchips, with implications for the reliability of these experiments. To overcome this critical issue, we developed new PDMS-free microdevices dedicated to live-cell imaging that show no interference with small molecules. They also integrate a module for maintaining precise sample temperature both above and below ambient as well as for rapid temperature shifts. Importantly, changes in medium composition and temperature can be efficiently achieved within the chips while recording cell behaviour by microscopy. Compatible with different model systems, our platforms provide a versatile solution for the dynamic regulation of the cellular environment during live-cell imaging. PMID:27512142

Critical Assessment of Small Molecule Identification 2016: automated methods.

PubMed

Schymanski, Emma L; Ruttkies, Christoph; Krauss, Martin; Brouard, Céline; Kind, Tobias; Dührkop, Kai; Allen, Felicity; Vaniya, Arpana; Verdegem, Dries; Böcker, Sebastian; Rousu, Juho; Shen, Huibin; Tsugawa, Hiroshi; Sajed, Tanvir; Fiehn, Oliver; Ghesquière, Bart; Neumann, Steffen

2017-03-27

The fourth round of the Critical Assessment of Small Molecule Identification (CASMI) Contest ( www.casmi-contest.org ) was held in 2016, with two new categories for automated methods. This article covers the 208 challenges in Categories 2 and 3, without and with metadata, from organization, participation, results and post-contest evaluation of CASMI 2016 through to perspectives for future contests and small molecule annotation/identification. The Input Output Kernel Regression (CSI:IOKR) machine learning approach performed best in "Category 2: Best Automatic Structural Identification-In Silico Fragmentation Only", won by Team Brouard with 41% challenge wins. The winner of "Category 3: Best Automatic Structural Identification-Full Information" was Team Kind (MS-FINDER), with 76% challenge wins. The best methods were able to achieve over 30% Top 1 ranks in Category 2, with all methods ranking the correct candidate in the Top 10 in around 50% of challenges. This success rate rose to 70% Top 1 ranks in Category 3, with candidates in the Top 10 in over 80% of the challenges. The machine learning and chemistry-based approaches are shown to perform in complementary ways. The improvement in (semi-)automated fragmentation methods for small molecule identification has been substantial. The achieved high rates of correct candidates in the Top 1 and Top 10, despite large candidate numbers, open up great possibilities for high-throughput annotation of untargeted analysis for "known unknowns". As more high quality training data becomes available, the improvements in machine learning methods will likely continue, but the alternative approaches still provide valuable complementary information. Improved integration of experimental context will also improve identification success further for "real life" annotations. The true "unknown unknowns" remain to be evaluated in future CASMI contests. Graphical abstract .

Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

PubMed Central

Tofoleanu, Florentina; Pickard, Frank C.; König, Gerhard; Huang, Jing; Damjanović, Ana; Baek, Minkyung; Seok, Chaok; Brooks, Bernard R.

2016-01-01

Herein, we report the absolute binding free energy calculations of CBClip complexes in the SAMPL5 blind challenge. Initial conformations of CBClip complexes were obtained using docking and molecular dynamics simulations. Free energy calculations were performed using thermodynamic integration (TI) with soft-core potentials and Bennett’s acceptance ratio (BAR) method based on a serial insertion scheme. We compared the results obtained with TI simulations with soft-core potentials and Hamiltonian replica exchange simulations with the serial insertion method combined with the BAR method. The results show that the difference between the two methods can be mainly attributed to the van der Waals free energies, suggesting that either the simulations used for TI or the simulations used for BAR, or both are not fully converged and the two sets of simulations may have sampled difference phase space regions. The penalty scores of force field parameters of the 10 guest molecules provided by CHARMM Generalized Force Field can be an indicator of the accuracy of binding free energy calculations. Among our submissions, the combination of docking and TI performed best, which yielded the root mean square deviation of 2.94 kcal/mol and an average unsigned error of 3.41 kcal/mol for the ten guest molecules. These values were best overall among all participants. However, our submissions had little correlation with experiments. PMID:27677749

Expression and Secretion of TNF-α in Mouse Taste Buds: A Novel Function of a Specific Subset of Type II Taste Cells

PubMed Central

Feng, Pu; Zhao, Hang; Chai, Jinghua; Huang, Liquan; Wang, Hong

2012-01-01

Taste buds are chemosensory structures widely distributed on the surface of the oral cavity and larynx. Taste cells, exposed to the oral environment, face great challenges in defense against potential pathogens. While immune cells, such as T-cells and macrophages, are rarely found in taste buds, high levels of expression of some immune-response-associated molecules are observed in taste buds. Yet, the cellular origins of these immune molecules such as cytokines in taste buds remain to be determined. Here, we show that a specific subset of taste cells selectively expresses high levels of the inflammatory cytokine tumor necrosis factor-α (TNF-α). Based on immuno-colocalization experiments using taste-cell-type markers, the TNF-α-producing cells are predominantly type II taste cells expressing the taste receptor T1R3. These cells can rapidly increase TNF-α production and secretion upon inflammatory challenges, both in vivo and in vitro. The lipopolysaccharide (LPS)-induced TNF-α expression in taste cells was completely eliminated in TLR2−/−/TLR4−/− double-gene-knockout mice, which confirms that the induction of TNF-α in taste buds by LPS is mediated through TLR signaling pathways. The taste-cell-produced TNF-α may contribute to local immune surveillance, as well as regulate taste sensation under normal and pathological conditions. PMID:22905218

Expression and secretion of TNF-α in mouse taste buds: a novel function of a specific subset of type II taste cells.

PubMed

Feng, Pu; Zhao, Hang; Chai, Jinghua; Huang, Liquan; Wang, Hong

2012-01-01

Taste buds are chemosensory structures widely distributed on the surface of the oral cavity and larynx. Taste cells, exposed to the oral environment, face great challenges in defense against potential pathogens. While immune cells, such as T-cells and macrophages, are rarely found in taste buds, high levels of expression of some immune-response-associated molecules are observed in taste buds. Yet, the cellular origins of these immune molecules such as cytokines in taste buds remain to be determined. Here, we show that a specific subset of taste cells selectively expresses high levels of the inflammatory cytokine tumor necrosis factor-α (TNF-α). Based on immuno-colocalization experiments using taste-cell-type markers, the TNF-α-producing cells are predominantly type II taste cells expressing the taste receptor T1R3. These cells can rapidly increase TNF-α production and secretion upon inflammatory challenges, both in vivo and in vitro. The lipopolysaccharide (LPS)-induced TNF-α expression in taste cells was completely eliminated in TLR2(-/-)/TLR4(-/-) double-gene-knockout mice, which confirms that the induction of TNF-α in taste buds by LPS is mediated through TLR signaling pathways. The taste-cell-produced TNF-α may contribute to local immune surveillance, as well as regulate taste sensation under normal and pathological conditions.

Single-molecule techniques in biophysics: a review of the progress in methods and applications.

PubMed

Miller, Helen; Zhou, Zhaokun; Shepherd, Jack; Wollman, Adam J M; Leake, Mark C

2018-02-01

Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.

Single-molecule techniques in biophysics: a review of the progress in methods and applications

NASA Astrophysics Data System (ADS)

Miller, Helen; Zhou, Zhaokun; Shepherd, Jack; Wollman, Adam J. M.; Leake, Mark C.

2018-02-01

Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in ‘force spectroscopy’ techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.

Molecular communication and networking: opportunities and challenges.

PubMed

Nakano, Tadashi; Moore, Michael J; Wei, Fang; Vasilakos, Athanasios V; Shuai, Jianwei

2012-06-01

The ability of engineered biological nanomachines to communicate with biological systems at the molecular level is anticipated to enable future applications such as monitoring the condition of a human body, regenerating biological tissues and organs, and interfacing artificial devices with neural systems. From the viewpoint of communication theory and engineering, molecular communication is proposed as a new paradigm for engineered biological nanomachines to communicate with the natural biological nanomachines which form a biological system. Distinct from the current telecommunication paradigm, molecular communication uses molecules as the carriers of information; sender biological nanomachines encode information on molecules and release the molecules in the environment, the molecules then propagate in the environment to receiver biological nanomachines, and the receiver biological nanomachines biochemically react with the molecules to decode information. Current molecular communication research is limited to small-scale networks of several biological nanomachines. Key challenges to bridge the gap between current research and practical applications include developing robust and scalable techniques to create a functional network from a large number of biological nanomachines. Developing networking mechanisms and communication protocols is anticipated to introduce new avenues into integrating engineered and natural biological nanomachines into a single networked system. In this paper, we present the state-of-the-art in the area of molecular communication by discussing its architecture, features, applications, design, engineering, and physical modeling. We then discuss challenges and opportunities in developing networking mechanisms and communication protocols to create a network from a large number of bio-nanomachines for future applications.

Structural distributions from single-molecule measurements as a tool for molecular mechanics

PubMed Central

Hanson, Jeffrey A.; Brokaw, Jason; Hayden, Carl C.; Chu, Jhih-Wei; Yang, Haw

2011-01-01

A mechanical view provides an attractive alternative for predicting the behavior of complex systems since it circumvents the resource-intensive requirements of atomistic models; however, it remains extremely challenging to characterize the mechanical responses of a system at the molecular level. Here, the structural distribution is proposed to be an effective means to extracting the molecular mechanical properties. End-to-end distance distributions for a series of short poly-L-proline peptides with the sequence PnCG3K-biotin (n = 8, 12, 15 and 24) were used to experimentally illustrate this new approach. High-resolution single-molecule Förster-type resonance energy transfer (FRET) experiments were carried out and the conformation-resolving power was characterized and discussed in the context of the conventional constant-time binning procedure for FRET data analysis. It was shown that the commonly adopted theoretical polymer models—including the worm-like chain, the freely jointed chain, and the self-avoiding chain—could not be distinguished by the averaged end-to-end distances, but could be ruled out using the molecular details gained by conformational distribution analysis because similar polymers of different sizes could respond to external forces differently. Specifically, by fitting the molecular conformational distribution to a semi-flexible polymer model, the effective persistence lengths for the series of short poly-L-proline peptides were found to be size-dependent with values of ~190 Å, ~67 Å, ~51 Å, and ~76 Å for n = 8, 12, 15, and 24, respectively. A comprehensive computational modeling was carried out to gain further insights for this surprising discovery. It was found that P8 exists as the extended all-trans isomaer whereas P12 and P15 predominantly contained one proline residue in the cis conformation. P24 exists as a mixture of one-cis (75%) and two-cis (25%) isomers where each isomer contributes to an experimentally resolvable conformational mode. This work demonstrates the resolving power of the distribution-based approach, and the capacity of integrating high-resolution single-molecule FRET experiments with molecular modeling to reveal detailed structural information about the conformation of molecules on the length scales relevant to the study of biological molecules. PMID:22661822

20180410 - Finding small molecules in big data (Analytica)

EPA Science Inventory

Metabolomics and exposomics are amongst the youngest and most dynamic of the omics disciplines. While the molecules involved are smaller than proteomics and the other, larger “omics”, the challenges are in many ways greater. Elements are less constrained, there are no...

Organic Materials in the Undergraduate Laboratory: Microscale Synthesis and Investigation of a Donor-Acceptor Molecule

ERIC Educational Resources Information Center

Pappenfus, Ted M.; Schliep, Karl B.; Dissanayake, Anudaththa; Ludden, Trevor; Nieto-Ortega, Belen; Lopez Navarrete, Juan T.; Ruiz Delgado, M. Carmen; Casado, Juan

2012-01-01

A series of experiments for undergraduate courses (e.g., organic, physical) have been developed in the area of small molecule organic materials. These experiments focus on understanding the electronic and redox properties of a donor-acceptor molecule that is prepared in a convenient one-step microscale reaction. The resulting intensely colored…

Spectroscopic characterization of Venus at the single molecule level.

PubMed

David, Charlotte C; Dedecker, Peter; De Cremer, Gert; Verstraeten, Natalie; Kint, Cyrielle; Michiels, Jan; Hofkens, Johan

2012-02-01

Venus is a recently developed, fast maturating, yellow fluorescent protein that has been used as a probe for in vivo applications. In the present work the photophysical characteristics of Venus were analyzed spectroscopically at the bulk and single molecule level. Through time-resolved single molecule measurements we found that single molecules of Venus display pronounced fluctuations in fluorescence emission, with clear fluorescence on- and off-times. These fluorescence intermittencies were found to occupy a broad range of time scales, ranging from milliseconds to several seconds. Such long off-times can complicate the analysis of single molecule counting experiments or single-molecule FRET experiments. This journal is © The Royal Society of Chemistry and Owner Societies 2012

Delocalization of frontier orbitals induced red emission for heptazine based thermally activated delayed fluorescence molecule: First-principles study

NASA Astrophysics Data System (ADS)

Kang, Yongxiang; Zhao, Liyun; Leng, Jiancai

2018-04-01

Design of red organic emitting molecules with characteristic of thermally activated delayed fluorescence (TADF) remains a great challenge. Here, electronic and optical properties of a series of multi-branched TADF molecules have been investigated based on the newly-proposed optimal Hartree-Fock percentage method. Results show that, though enlarging the delocalization of HOMO and LUMO, the emission wavelength is redshift. The designed red TADF molecule possesses smaller reorganization energy than these for reported molecules. This indicates the non-radiative energy consumption of excited state is small and effective luminescence can be expected. Thus, a promising red thermally activated delayed fluorescence molecule is proposed.

Simulation of FRET dyes allows quantitative comparison against experimental data

NASA Astrophysics Data System (ADS)

Reinartz, Ines; Sinner, Claude; Nettels, Daniel; Stucki-Buchli, Brigitte; Stockmar, Florian; Panek, Pawel T.; Jacob, Christoph R.; Nienhaus, Gerd Ulrich; Schuler, Benjamin; Schug, Alexander

2018-03-01

Fully understanding biomolecular function requires detailed insight into the systems' structural dynamics. Powerful experimental techniques such as single molecule Förster Resonance Energy Transfer (FRET) provide access to such dynamic information yet have to be carefully interpreted. Molecular simulations can complement these experiments but typically face limits in accessing slow time scales and large or unstructured systems. Here, we introduce a coarse-grained simulation technique that tackles these challenges. While requiring only few parameters, we maintain full protein flexibility and include all heavy atoms of proteins, linkers, and dyes. We are able to sufficiently reduce computational demands to simulate large or heterogeneous structural dynamics and ensembles on slow time scales found in, e.g., protein folding. The simulations allow for calculating FRET efficiencies which quantitatively agree with experimentally determined values. By providing atomically resolved trajectories, this work supports the planning and microscopic interpretation of experiments. Overall, these results highlight how simulations and experiments can complement each other leading to new insights into biomolecular dynamics and function.

Observation of Binding and Rotation of Methane and Hydrogen within a Functional Metal–Organic Framework

PubMed Central

2016-01-01

The key requirement for a portable store of natural gas is to maximize the amount of gas within the smallest possible space. The packing of methane (CH4) in a given storage medium at the highest possible density is, therefore, a highly desirable but challenging target. We report a microporous hydroxyl-decorated material, MFM-300(In) (MFM = Manchester Framework Material, replacing the NOTT designation), which displays a high volumetric uptake of 202 v/v at 298 K and 35 bar for CH4 and 488 v/v at 77 K and 20 bar for H2. Direct observation and quantification of the location, binding, and rotational modes of adsorbed CH4 and H2 molecules within this host have been achieved, using neutron diffraction and inelastic neutron scattering experiments, coupled with density functional theory (DFT) modeling. These complementary techniques reveal a very efficient packing of H2 and CH4 molecules within MFM-300(In), reminiscent of the condensed gas in pure component crystalline solids. We also report here, for the first time, the experimental observation of a direct binding interaction between adsorbed CH4 molecules and the hydroxyl groups within the pore of a material. This is different from the arrangement found in CH4/water clathrates, the CH4 store of nature. PMID:27410670

Heterologous expression of the plant cysteine protease bromelain and its inhibitor in Pichia pastoris.

PubMed

Luniak, Nora; Meiser, Peter; Burkart, Sonja; Müller, Rolf

2017-01-01

Expression of proteases in heterologous hosts remains an ambitious challenge due to severe problems associated with digestion of host proteins. On the other hand, proteases are broadly used in industrial applications and resemble promising drug candidates. Bromelain is an herbal drug that is medicinally used for treatment of oedematous swellings and inflammatory conditions and consists in large part of proteolytic enzymes. Even though various experiments underline the requirement of active cysteine proteases for biological activity, so far no investigation succeeded to clearly clarify the pharmacological mode of action of bromelain. The potential role of proteases themselves and other molecules of this multi-component extract currently remain largely unknown or ill defined. Here, we set out to express several bromelain cysteine proteases as well as a bromelain inhibitor molecule in order to gain defined molecular entities for subsequent studies. After cloning the genes from its natural source Ananas comosus (pineapple plant) into Pichia pastoris and subsequent fermentation and purification, we obtained active protease and inhibitor molecules which were subsequently biochemically characterized. Employing purified bromelain fractions paves the way for further elucidation of pharmacological activities of this natural product. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:54-65, 2017. © 2016 American Institute of Chemical Engineers.

Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa

PubMed Central

Ridder, Lars; van der Hooft, Justin J. J.; Verhoeven, Stefan

2014-01-01

The MAGMa software for automatic annotation of mass spectrometry based fragmentation data was applied to 16 MS/MS datasets of the CASMI 2013 contest. Eight solutions were submitted in category 1 (molecular formula assignments) and twelve in category 2 (molecular structure assignment). The MS/MS peaks of each challenge were matched with in silico generated substructures of candidate molecules from PubChem, resulting in penalty scores that were used for candidate ranking. In 6 of the 12 submitted solutions in category 2, the correct chemical structure obtained the best score, whereas 3 molecules were ranked outside the top 5. All top ranked molecular formulas submitted in category 1 were correct. In addition, we present MAGMa results generated retrospectively for the remaining challenges. Successful application of the MAGMa algorithm required inclusion of the relevant candidate molecules, application of the appropriate mass tolerance and a sufficient degree of in silico fragmentation of the candidate molecules. Furthermore, the effect of the exhaustiveness of the candidate lists and limitations of substructure based scoring are discussed. PMID:26819876

Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa.

PubMed

Ridder, Lars; van der Hooft, Justin J J; Verhoeven, Stefan

2014-01-01

The MAGMa software for automatic annotation of mass spectrometry based fragmentation data was applied to 16 MS/MS datasets of the CASMI 2013 contest. Eight solutions were submitted in category 1 (molecular formula assignments) and twelve in category 2 (molecular structure assignment). The MS/MS peaks of each challenge were matched with in silico generated substructures of candidate molecules from PubChem, resulting in penalty scores that were used for candidate ranking. In 6 of the 12 submitted solutions in category 2, the correct chemical structure obtained the best score, whereas 3 molecules were ranked outside the top 5. All top ranked molecular formulas submitted in category 1 were correct. In addition, we present MAGMa results generated retrospectively for the remaining challenges. Successful application of the MAGMa algorithm required inclusion of the relevant candidate molecules, application of the appropriate mass tolerance and a sufficient degree of in silico fragmentation of the candidate molecules. Furthermore, the effect of the exhaustiveness of the candidate lists and limitations of substructure based scoring are discussed.

Challenges and Opportunities for Small-Molecule Fluorescent Probes in Redox Biology Applications.

PubMed

Jiang, Xiqian; Wang, Lingfei; Carroll, Shaina L; Chen, Jianwei; Wang, Meng C; Wang, Jin

2018-02-16

The concentrations of reactive oxygen/nitrogen species (ROS/RNS) are critical to various biochemical processes. Small-molecule fluorescent probes have been widely used to detect and/or quantify ROS/RNS in many redox biology studies and serve as an important complementary to protein-based sensors with unique applications. Recent Advances: New sensing reactions have emerged in probe development, allowing more selective and quantitative detection of ROS/RNS, especially in live cells. Improvements have been made in sensing reactions, fluorophores, and bioavailability of probe molecules. In this review, we will not only summarize redox-related small-molecule fluorescent probes but also lay out the challenges of designing probes to help redox biologists independently evaluate the quality of reported small-molecule fluorescent probes, especially in the chemistry literature. We specifically highlight the advantages of reversibility in sensing reactions and its applications in ratiometric probe design for quantitative measurements in living cells. In addition, we compare the advantages and disadvantages of small-molecule probes and protein-based probes. The low physiological relevant concentrations of most ROS/RNS call for new sensing reactions with better selectivity, kinetics, and reversibility; fluorophores with high quantum yield, wide wavelength coverage, and Stokes shifts; and structural design with good aqueous solubility, membrane permeability, low protein interference, and organelle specificity. Antioxid. Redox Signal. 00, 000-000.

Rationalizing the permeation of polar antibiotics into Gram-negative bacteria.

PubMed

Scorciapino, Mariano Andrea; Acosta-Gutierrez, Silvia; Benkerrou, Dehbia; D'Agostino, Tommaso; Malloci, Giuliano; Samanta, Susruta; Bodrenko, Igor; Ceccarelli, Matteo

2017-03-22

The increasing level of antibiotic resistance in Gram-negative bacteria, together with the lack of new potential drug scaffolds in the pipeline, make the problem of infectious diseases a global challenge for modern medicine. The main reason that Gram-negative bacteria are particularly challenging is the presence of an outer cell-protecting membrane, which is not present in Gram-positive species. Such an asymmetric bilayer is a highly effective barrier for polar molecules. Several protein systems are expressed in the outer membrane to control the internal concentration of both nutrients and noxious species, in particular: (i) water-filled channels that modulate the permeation of polar molecules and ions according to concentration gradients, and (ii) efflux pumps to actively expel toxic compounds. Thus, besides expressing specific enzymes for drugs degradation, Gram-negative bacteria can also resist by modulating the influx and efflux of antibiotics, keeping the internal concentration low. However, there are no direct and robust experimental methods capable of measuring the permeability of small molecules, thus severely limiting our knowledge of the molecular mechanisms that ultimately control the permeation of antibiotics through the outer membrane. This is the innovation gap to be filled for Gram-negative bacteria. This review is focused on the permeation of small molecules through porins, considered the main path for the entry of polar antibiotics into Gram-negative bacteria. A fundamental understanding of how these proteins are able to filter small molecules is a prerequisite to design/optimize antibacterials with improved permeation. The level of sophistication of modern molecular modeling algorithms and the advances in new computer hardware has made the simulation of such complex processes possible at the molecular level. In this work we aim to share our experience and perspectives in the context of a multidisciplinary extended collaboration within the IMI-Translocation consortium. The synergistic combination of structural data, in vitro assays and computer simulations has proven to give new insights towards the identification and description of physico-chemical properties modulating permeation. Once similar general rules are identified, we believe that the use of virtual screening techniques will be very helpful in searching for new molecular scaffolds with enhanced permeation, and that molecular modeling will be of fundamental assistance to the optimization stage.

Rationalizing the permeation of polar antibiotics into Gram-negative bacteria

NASA Astrophysics Data System (ADS)

Scorciapino, Mariano Andrea; Acosta-Gutierrez, Silvia; Benkerrou, Dehbia; D'Agostino, Tommaso; Malloci, Giuliano; Samanta, Susruta; Bodrenko, Igor; Ceccarelli, Matteo

2017-03-01

The increasing level of antibiotic resistance in Gram-negative bacteria, together with the lack of new potential drug scaffolds in the pipeline, make the problem of infectious diseases a global challenge for modern medicine. The main reason that Gram-negative bacteria are particularly challenging is the presence of an outer cell-protecting membrane, which is not present in Gram-positive species. Such an asymmetric bilayer is a highly effective barrier for polar molecules. Several protein systems are expressed in the outer membrane to control the internal concentration of both nutrients and noxious species, in particular: (i) water-filled channels that modulate the permeation of polar molecules and ions according to concentration gradients, and (ii) efflux pumps to actively expel toxic compounds. Thus, besides expressing specific enzymes for drugs degradation, Gram-negative bacteria can also resist by modulating the influx and efflux of antibiotics, keeping the internal concentration low. However, there are no direct and robust experimental methods capable of measuring the permeability of small molecules, thus severely limiting our knowledge of the molecular mechanisms that ultimately control the permeation of antibiotics through the outer membrane. This is the innovation gap to be filled for Gram-negative bacteria. This review is focused on the permeation of small molecules through porins, considered the main path for the entry of polar antibiotics into Gram-negative bacteria. A fundamental understanding of how these proteins are able to filter small molecules is a prerequisite to design/optimize antibacterials with improved permeation. The level of sophistication of modern molecular modeling algorithms and the advances in new computer hardware has made the simulation of such complex processes possible at the molecular level. In this work we aim to share our experience and perspectives in the context of a multidisciplinary extended collaboration within the IMI-Translocation consortium. The synergistic combination of structural data, in vitro assays and computer simulations has proven to give new insights towards the identification and description of physico-chemical properties modulating permeation. Once similar general rules are identified, we believe that the use of virtual screening techniques will be very helpful in searching for new molecular scaffolds with enhanced permeation, and that molecular modeling will be of fundamental assistance to the optimization stage.

A Single-Molecule Barcoding System using Nanoslits for DNA Analysis

NASA Astrophysics Data System (ADS)

Jo, Kyubong; Schramm, Timothy M.; Schwartz, David C.

Single DNA molecule approaches are playing an increasingly central role in the analytical genomic sciences because single molecule techniques intrinsically provide individualized measurements of selected molecules, free from the constraints of bulk techniques, which blindly average noise and mask the presence of minor analyte components. Accordingly, a principal challenge that must be addressed by all single molecule approaches aimed at genome analysis is how to immobilize and manipulate DNA molecules for measurements that foster construction of large, biologically relevant data sets. For meeting this challenge, this chapter discusses an integrated approach for microfabricated and nanofabricated devices for the manipulation of elongated DNA molecules within nanoscale geometries. Ideally, large DNA coils stretch via nanoconfinement when channel dimensions are within tens of nanometers. Importantly, stretched, often immobilized, DNA molecules spanning hundreds of kilobase pairs are required by all analytical platforms working with large genomic substrates because imaging techniques acquire sequence information from molecules that normally exist in free solution as unrevealing random coils resembling floppy balls of yarn. However, nanoscale devices fabricated with sufficiently small dimensions fostering molecular stretching make these devices impractical because of the requirement of exotic fabrication technologies, costly materials, and poor operational efficiencies. In this chapter, such problems are addressed by discussion of a new approach to DNA presentation and analysis that establishes scaleable nanoconfinement conditions through reduction of ionic strength; stiffening DNA molecules thus enabling their arraying for analysis using easily fabricated devices that can also be mass produced. This new approach to DNA nanoconfinement is complemented by the development of a novel labeling scheme for reliable marking of individual molecules with fluorochrome labels, creating molecular barcodes, which are efficiently read using fluorescence resonance energy transfer techniques for minimizing noise from unincorporated labels. As such, our integrative approach for the realization of genomic analysis through nanoconfinement, named nanocoding, was demonstrated through the barcoding and mapping of bacterial artificial chromosomal molecules, thereby providing the basis for a high-throughput platform competent for whole genome investigations.

Proposal for probing energy transfer pathway by single-molecule pump-dump experiment.

PubMed

Tao, Ming-Jie; Ai, Qing; Deng, Fu-Guo; Cheng, Yuan-Chung

2016-06-09

The structure of Fenna-Matthews-Olson (FMO) light-harvesting complex had long been recognized as containing seven bacteriochlorophyll (BChl) molecules. Recently, an additional BChl molecule was discovered in the crystal structure of the FMO complex, which may serve as a link between baseplate and the remaining seven molecules. Here, we investigate excitation energy transfer (EET) process by simulating single-molecule pump-dump experiment in the eight-molecules complex. We adopt the coherent modified Redfield theory and non-Markovian quantum jump method to simulate EET dynamics. This scheme provides a practical approach of detecting the realistic EET pathway in BChl complexes with currently available experimental technology. And it may assist optimizing design of artificial light-harvesting devices.

Proposal for probing energy transfer pathway by single-molecule pump-dump experiment

NASA Astrophysics Data System (ADS)

Tao, Ming-Jie; Ai, Qing; Deng, Fu-Guo; Cheng, Yuan-Chung

2016-06-01

The structure of Fenna-Matthews-Olson (FMO) light-harvesting complex had long been recognized as containing seven bacteriochlorophyll (BChl) molecules. Recently, an additional BChl molecule was discovered in the crystal structure of the FMO complex, which may serve as a link between baseplate and the remaining seven molecules. Here, we investigate excitation energy transfer (EET) process by simulating single-molecule pump-dump experiment in the eight-molecules complex. We adopt the coherent modified Redfield theory and non-Markovian quantum jump method to simulate EET dynamics. This scheme provides a practical approach of detecting the realistic EET pathway in BChl complexes with currently available experimental technology. And it may assist optimizing design of artificial light-harvesting devices.

Proposal for probing energy transfer pathway by single-molecule pump-dump experiment

PubMed Central

Tao, Ming-Jie; Ai, Qing; Deng, Fu-Guo; Cheng, Yuan-Chung

2016-01-01

The structure of Fenna-Matthews-Olson (FMO) light-harvesting complex had long been recognized as containing seven bacteriochlorophyll (BChl) molecules. Recently, an additional BChl molecule was discovered in the crystal structure of the FMO complex, which may serve as a link between baseplate and the remaining seven molecules. Here, we investigate excitation energy transfer (EET) process by simulating single-molecule pump-dump experiment in the eight-molecules complex. We adopt the coherent modified Redfield theory and non-Markovian quantum jump method to simulate EET dynamics. This scheme provides a practical approach of detecting the realistic EET pathway in BChl complexes with currently available experimental technology. And it may assist optimizing design of artificial light-harvesting devices. PMID:27277702

Theory of single-molecule controlled rotation experiments, predictions, tests, and comparison with stalling experiments in F1-ATPase.

PubMed

Volkán-Kacsó, Sándor; Marcus, Rudolph A

2016-10-25

A recently proposed chemomechanical group transfer theory of rotary biomolecular motors is applied to treat single-molecule controlled rotation experiments. In these experiments, single-molecule fluorescence is used to measure the binding and release rate constants of nucleotides by monitoring the occupancy of binding sites. It is shown how missed events of nucleotide binding and release in these experiments can be corrected using theory, with F 1 -ATP synthase as an example. The missed events are significant when the reverse rate is very fast. Using the theory the actual rate constants in the controlled rotation experiments and the corrections are predicted from independent data, including other single-molecule rotation and ensemble biochemical experiments. The effective torsional elastic constant is found to depend on the binding/releasing nucleotide, and it is smaller for ADP than for ATP. There is a good agreement, with no adjustable parameters, between the theoretical and experimental results of controlled rotation experiments and stalling experiments, for the range of angles where the data overlap. This agreement is perhaps all the more surprising because it occurs even though the binding and release of fluorescent nucleotides is monitored at single-site occupancy concentrations, whereas the stalling and free rotation experiments have multiple-site occupancy.

Beyond experimental noise: Analyzing single-molecule data of heterogeneous systems. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

NASA Astrophysics Data System (ADS)

Meroz, Yasmine

2015-06-01

In the 1980s the world witnessed the advent of single-molecule experiments. The first atomic resolution characterization of a surface was reported by scanning tunneling microscope (STM) in 1982 [1], followed by atomic force microscope (AFM) in 1986 [2]. The first optical detection and spectroscopy of a single molecule in a solid took place in 1989 [3,4], in a time where essentially all chemical experiments were made on bulk, i.e. averaging over millions of copies of the same molecule.

Single-Molecule Tracking and Its Application in Biomolecular Binding Detection.

PubMed

Liu, Cong; Liu, Yen-Liang; Perillo, Evan P; Dunn, Andrew K; Yeh, Hsin-Chih

2016-01-01

In the past two decades significant advances have been made in single-molecule detection, which enables the direct observation of single biomolecules at work in real time and under physiological conditions. In particular, the development of single-molecule tracking (SMT) microscopy allows us to monitor the motion paths of individual biomolecules in living systems, unveiling the localization dynamics and transport modalities of the biomolecules that support the development of life. Beyond the capabilities of traditional camera-based tracking techniques, state-of-the-art SMT microscopies developed in recent years can record fluorescence lifetime while tracking a single molecule in the 3D space. This multiparameter detection capability can open the door to a wide range of investigations at the cellular or tissue level, including identification of molecular interaction hotspots and characterization of association/dissociation kinetics between molecules. In this review, we discuss various SMT techniques developed to date, with an emphasis on our recent development of the next generation 3D tracking system that not only achieves ultrahigh spatiotemporal resolution but also provides sufficient working depth suitable for live animal imaging. We also discuss the challenges that current SMT techniques are facing and the potential strategies to tackle those challenges.

Single-Molecule Tracking and Its Application in Biomolecular Binding Detection

PubMed Central

Liu, Cong; Liu, Yen-Liang; Perillo, Evan P.; Dunn, Andrew K.; Yeh, Hsin-Chih

2016-01-01

In the past two decades significant advances have been made in single-molecule detection, which enables the direct observation of single biomolecules at work in real time and under physiological conditions. In particular, the development of single-molecule tracking (SMT) microscopy allows us to monitor the motion paths of individual biomolecules in living systems, unveiling the localization dynamics and transport modalities of the biomolecules that support the development of life. Beyond the capabilities of traditional camera-based tracking techniques, state-of-the-art SMT microscopies developed in recent years can record fluorescence lifetime while tracking a single molecule in the 3D space. This multiparameter detection capability can open the door to a wide range of investigations at the cellular or tissue level, including identification of molecular interaction hotspots and characterization of association/dissociation kinetics between molecules. In this review, we discuss various SMT techniques developed to date, with an emphasis on our recent development of the next generation 3D tracking system that not only achieves ultrahigh spatiotemporal resolution but also provides sufficient working depth suitable for live animal imaging. We also discuss the challenges that current SMT techniques are facing and the potential strategies to tackle those challenges. PMID:27660404

Experiences in fragment-based drug discovery.

PubMed

Murray, Christopher W; Verdonk, Marcel L; Rees, David C

2012-05-01

Fragment-based drug discovery (FBDD) has become established in both industry and academia as an alternative approach to high-throughput screening for the generation of chemical leads for drug targets. In FBDD, specialised detection methods are used to identify small chemical compounds (fragments) that bind to the drug target, and structural biology is usually employed to establish their binding mode and to facilitate their optimisation. In this article, we present three recent and successful case histories in FBDD. We then re-examine the key concepts and challenges of FBDD with particular emphasis on recent literature and our own experience from a substantial number of FBDD applications. Our opinion is that careful application of FBDD is living up to its promise of delivering high quality leads with good physical properties and that in future many drug molecules will be derived from fragment-based approaches. Copyright © 2012 Elsevier Ltd. All rights reserved.

Large scale rigidity-based flexibility analysis of biomolecules

PubMed Central

Streinu, Ileana

2016-01-01

KINematics And RIgidity (KINARI) is an on-going project for in silico flexibility analysis of proteins. The new version of the software, Kinari-2, extends the functionality of our free web server KinariWeb, incorporates advanced web technologies, emphasizes the reproducibility of its experiments, and makes substantially improved tools available to the user. It is designed specifically for large scale experiments, in particular, for (a) very large molecules, including bioassemblies with high degree of symmetry such as viruses and crystals, (b) large collections of related biomolecules, such as those obtained through simulated dilutions, mutations, or conformational changes from various types of dynamics simulations, and (c) is intended to work as seemlessly as possible on the large, idiosyncratic, publicly available repository of biomolecules, the Protein Data Bank. We describe the system design, along with the main data processing, computational, mathematical, and validation challenges underlying this phase of the KINARI project. PMID:26958583

Investigating single molecule adhesion by atomic force spectroscopy.

PubMed

Stetter, Frank W S; Kienle, Sandra; Krysiak, Stefanie; Hugel, Thorsten

2015-02-27

Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment.

Investigating Single Molecule Adhesion by Atomic Force Spectroscopy

PubMed Central

Stetter, Frank W. S.; Kienle, Sandra; Krysiak, Stefanie; Hugel, Thorsten

2015-01-01

Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment. PMID:25867282

Poster 11: Simulating the VUV photochemistry in the upper atmosphere of Titan

NASA Astrophysics Data System (ADS)

Tigrine, Sarah; Carrasco, Nathalie; Vettier, Ludovic; Cernogora, Guy

2016-06-01

The Cassini mission around Titan revealed that the interaction between the N2 and CH4 molecules and the solar VUV radiation leads to a complex chemistry above an altitude of 800 km with the detection of heavy organic molecules like benzene (C6H6). This is consistent with an initiation of the aerosols in Titan's upper atmosphere. The presence of those molecules makes Titan a natural laboratory to witness and understand prebiotic-like chemistry but despite all the data collected, all the possible photochemical processes in such a hydrocarbon-nitrogen-rich environment are not precisely understood. This is why Titan's atmospheric chemistry experiments are of high interest, especially those focusing on the photochemistry as most of the Titan-like experiments are based on N2-CH4 plasma techniques. In order to reproduce this VUV photochemistry of N2 and CH4, we designed a photochemical reactor named APSIS which is to be coupled window-less with a VUV photon source as N2 needs wavelengths shorter than 100 nm in order to be dissociated. Those wavelengths are available at synchrotron beamlines but are challenging to obtain with common laboratory discharge lamps. At LATMOS, we developed a table-top VUV window-less source using noble gases for the micro-wave discharge. We started with Neon, as it has two resonance lines at 73.6 and 74.3 nm which allow us to dissociate and/or ionize both CH4 and N2. We will present here our first experimental results obtained with APSIS coupled with this VUV source and then discuss them regarding the Cassini data and other previous laboratory photochemical studies.

Induction of Protective Immune Responses Against Schistosomiasis haematobium in Hamsters and Mice Using Cysteine Peptidase-Based Vaccine

PubMed Central

Tallima, Hatem; Dalton, John P.; El Ridi, Rashika

2015-01-01

One of the major lessons we learned from the radiation-attenuated cercariae vaccine studies is that protective immunity against schistosomiasis is dependent on the induction of T helper (Th)1-/Th2-related immune responses. Since most schistosome larval and adult-worm-derived molecules used for vaccination uniformly induce a polarized Th1 response, it was essential to include a type 2 immune response-inducing molecule, such as cysteine peptidases, in the vaccine formula. Here, we demonstrate that a single subcutaneous injection of Syrian hamsters with 200 μg active papain, 1 h before percutaneous exposure to 150 cercariae of Schistosoma haematobium, led to highly significant (P < 0.005) reduction of >50% in worm burden and worm egg counts in intestine. Immunization of hamsters with 20 μg recombinant glyceraldehyde 3-phosphate dehydrogenase (rSG3PDH) and 20 μg 2-cys peroxiredoxin-derived peptide in a multiple antigen peptide construct (PRX MAP) together with papain (20 μg/hamster), as adjuvant led to considerable (64%) protection against challenge S. haematobium infection, similar to the levels reported with irradiated cercariae. Cysteine peptidases-based vaccination was also effective in protecting outbred mice against a percutaneous challenge infection with S. haematobium cercariae. In two experiments, a mixture of Schistosoma mansoni cathepsin B1 (SmCB1) and Fasciola hepatica cathepsin L1 (FhCL1) led to highly significant (P < 0.005) reduction of 70% in challenge S. haematobium worm burden and 60% reduction in liver egg counts. Mice vaccinated with SmCB1/FhCL1/rSG3PDH mixture and challenged with S. haematobium cercariae 3 weeks after the second immunization displayed highly significant (P < 0.005) reduction of 72% in challenge worm burden and no eggs in liver of 8–10 mice/group, as compared to unimmunized mice, associated with production of a mixture of type 1- and type 2-related cytokines and antibody responses. PMID:25852696

Students' Use of Three Different Visual Representations to Interpret Whether Molecules Are Polar or Nonpolar

ERIC Educational Resources Information Center

Host, Gunnar E.; Schonborn, Konrad J.; Palmerius, Karljohan E. Lundin

2012-01-01

Visualizing molecular properties is often crucial for constructing conceptual understanding in chemistry. However, research has revealed numerous challenges surrounding students' meaningful interpretation of the relationship between the geometry and electrostatic properties of molecules. This study explored students' (n = 18) use of three visual…

Mercury monohalides: suitability for electron electric dipole moment searches.

PubMed

Prasannaa, V S; Vutha, A C; Abe, M; Das, B P

2015-05-08

Heavy polar diatomic molecules are the primary tools for searching for the T-violating permanent electric dipole moment of the electron (eEDM). Valence electrons in some molecules experience extremely large effective electric fields due to relativistic interactions. These large effective electric fields are crucial to the success of polar-molecule-based eEDM search experiments. Here we report on the results of relativistic ab initio calculations of the effective electric fields in a series of molecules that are highly sensitive to an eEDM, the mercury monohalides (HgF, HgCl, HgBr, and HgI). We study the influence of the halide anions on E_{eff}, and identify HgBr and HgI as attractive candidates for future electric dipole moment search experiments.

Computation of Chemical Shifts for Paramagnetic Molecules: A Laboratory Experiment for the Undergraduate Curriculum

ERIC Educational Resources Information Center

Pritchard, Benjamin P.; Simpson, Scott; Zurek, Eva; Autschbach, Jochen

2014-01-01

A computational experiment investigating the [superscript 1]H and [superscript 13]C nuclear magnetic resonance (NMR) chemical shifts of molecules with unpaired electrons has been developed and implemented. This experiment is appropriate for an upper-level undergraduate laboratory course in computational, physical, or inorganic chemistry. The…

In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor.

PubMed

Lenselink, Eelke B; Beuming, Thijs; van Veen, Corine; Massink, Arnault; Sherman, Woody; van Vlijmen, Herman W T; IJzerman, Adriaan P

2016-10-01

In this work, we present a case study to explore the challenges associated with finding novel molecules for a receptor that has been studied in depth and has a wealth of chemical information available. Specifically, we apply a previously described protocol that incorporates explicit water molecules in the ligand binding site to prospectively screen over 2.5 million drug-like and lead-like compounds from the commercially available eMolecules database in search of novel binders to the adenosine A 2A receptor (A 2A AR). A total of seventy-one compounds were selected for purchase and biochemical assaying based on high ligand efficiency and high novelty (Tanimoto coefficient ≤0.25 to any A 2A AR tested compound). These molecules were then tested for their affinity to the adenosine A 2A receptor in a radioligand binding assay. We identified two hits that fulfilled the criterion of ~50 % radioligand displacement at a concentration of 10 μM. Next we selected an additional eight novel molecules that were predicted to make a bidentate interaction with Asn253 6.55 , a key interacting residue in the binding pocket of the A 2A AR. None of these eight molecules were found to be active. Based on these results we discuss the advantages of structure-based methods and the challenges associated with finding chemically novel molecules for well-explored targets.

Multi-Scale Modeling to Improve Single-Molecule, Single-Cell Experiments

NASA Astrophysics Data System (ADS)

Munsky, Brian; Shepherd, Douglas

2014-03-01

Single-cell, single-molecule experiments are producing an unprecedented amount of data to capture the dynamics of biological systems. When integrated with computational models, observations of spatial, temporal and stochastic fluctuations can yield powerful quantitative insight. We concentrate on experiments that localize and count individual molecules of mRNA. These high precision experiments have large imaging and computational processing costs, and we explore how improved computational analyses can dramatically reduce overall data requirements. In particular, we show how analyses of spatial, temporal and stochastic fluctuations can significantly enhance parameter estimation results for small, noisy data sets. We also show how full probability distribution analyses can constrain parameters with far less data than bulk analyses or statistical moment closures. Finally, we discuss how a systematic modeling progression from simple to more complex analyses can reduce total computational costs by orders of magnitude. We illustrate our approach using single-molecule, spatial mRNA measurements of Interleukin 1-alpha mRNA induction in human THP1 cells following stimulation. Our approach could improve the effectiveness of single-molecule gene regulation analyses for many other process.

Science& Technology Review December 2002

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

Budil, K S

2002-10-28

This issue has the following articles: (1) ''Doing It All: Sustaining Our Working Solutions, Rising to New Challenges''; (2) ''Emerging from the Cold War: Stockpile Stewardship and Beyond''--When the Cold War ended, Lawrence Livermore stepped up to a new national challenge--maintaining the safety and reliability of the U.S. nuclear stockpile without underground testing. (3) ''Machines from Interlocking Molecules''--Fundamental chemistry and physics research will enable scientists to control and use individual molecules. (4) ''Laser Zaps Communication Bottleneck''--Using laser communications, the U.S. military will be able to transmit data from advanced remote sensors in real time.

Challenges and recent advances in mass spectrometric imaging of neurotransmitters

PubMed Central

Gemperline, Erin; Chen, Bingming; Li, Lingjun

2014-01-01

Mass spectrometric imaging (MSI) is a powerful tool that grants the ability to investigate a broad mass range of molecules, from small molecules to large proteins, by creating detailed distribution maps of selected compounds. To date, MSI has demonstrated its versatility in the study of neurotransmitters and neuropeptides of different classes toward investigation of neurobiological functions and diseases. These studies have provided significant insight in neurobiology over the years and current technical advances are facilitating further improvements in this field. neurotransmitters, focusing specifically on the challenges and recent Herein, we advances of MSI of neurotransmitters. PMID:24568355

Extracting physics of life at the molecular level: A review of single-molecule data analyses.

PubMed

Colomb, Warren; Sarkar, Susanta K

2015-06-01

Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

Voltage-Driven Conformational Switching with Distinct Raman Signature in a Single-Molecule Junction.

PubMed

Bi, Hai; Palma, Carlos-Andres; Gong, Yuxiang; Hasch, Peter; Elbing, Mark; Mayor, Marcel; Reichert, Joachim; Barth, Johannes V

2018-04-11

Precisely controlling well-defined, stable single-molecule junctions represents a pillar of single-molecule electronics. Early attempts to establish computing with molecular switching arrays were partly challenged by limitations in the direct chemical characterization of metal-molecule-metal junctions. While cryogenic scanning probe studies have advanced the mechanistic understanding of current- and voltage-induced conformational switching, metal-molecule-metal conformations are still largely inferred from indirect evidence. Hence, the development of robust, chemically sensitive techniques is instrumental for advancement in the field. Here we probe the conformation of a two-state molecular switch with vibrational spectroscopy, while simultaneously operating it by means of the applied voltage. Our study emphasizes measurements of single-molecule Raman spectra in a room-temperature stable single-molecule switch presenting a signal modulation of nearly 2 orders of magnitude.

Single-Molecule Plasmon Sensing: Current Status and Future Prospects

PubMed Central

2017-01-01

Single-molecule detection has long relied on fluorescent labeling with high quantum-yield fluorophores. Plasmon-enhanced detection circumvents the need for labeling by allowing direct optical detection of weakly emitting and completely nonfluorescent species. This review focuses on recent advances in single molecule detection using plasmonic metal nanostructures as a sensing platform, particularly using a single particle–single molecule approach. In the past decade two mechanisms for plasmon-enhanced single-molecule detection have been demonstrated: (1) by plasmonically enhancing the emission of weakly fluorescent biomolecules, or (2) by monitoring shifts of the plasmon resonance induced by single-molecule interactions. We begin with a motivation regarding the importance of single molecule detection, and advantages plasmonic detection offers. We describe both detection mechanisms and discuss challenges and potential solutions. We finalize by highlighting the exciting possibilities in analytical chemistry and medical diagnostics. PMID:28762723

Probe-based measurement of lateral single-electron transfer between individual molecules

PubMed Central

Steurer, Wolfram; Fatayer, Shadi; Gross, Leo; Meyer, Gerhard

2015-01-01

The field of molecular electronics aims at using single molecules as functional building blocks for electronics components, such as switches, rectifiers or transistors. A key challenge is to perform measurements with atomistic control over the alignment of the molecule and its contacting electrodes. Here we use atomic force microscopy to examine charge transfer between weakly coupled pentacene molecules on insulating films with single-electron sensitivity and control over the atomistic details. We show that, in addition to the imaging capability, the probe tip can be used to control the charge state of individual molecules and to detect charge transfers to/from the tip, as well as between individual molecules. Our approach represents a novel route for molecular charge transfer studies with a host of opportunities, especially in combination with single atom/molecule manipulation and nanopatterning techniques. PMID:26387533

Circularly Polarized Luminescence from Simple Organic Molecules

PubMed Central

Sánchez-Carnerero, Esther M.; Agarrabeitia, Antonia R.; Moreno, Florencio; Maroto, Beatriz L.; Muller, Gilles; Ortiz, María J.

2015-01-01

This article aims to show the identity of “CPL-active simple organic molecules” as a new concept in Organic Chemistry due to the potential interest of these molecules, as availed by the exponentially growing number of research articles related to them. In particular, it describes and highlights the interest and difficulty in developing chiral simple (small and nonaggregated) organic molecules able to emit left- or right-circularly polarized light efficiently, the efforts realized up to now to reach this challenging objective, and the most significant milestones achieved to date. General guidelines for the preparation of these interesting molecules are also presented. PMID:26136234

Circularly Polarized Luminescence from Simple Organic Molecules.

PubMed

Sánchez-Carnerero, Esther M; Agarrabeitia, Antonia R; Moreno, Florencio; Maroto, Beatriz L; Muller, Gilles; Ortiz, María J; de la Moya, Santiago

2015-09-21

This article aims to show the identity of "circularly polarized luminescent active simple organic molecules" as a new concept in organic chemistry due to the potential interest of these molecules, as availed by the exponentially growing number of research articles related to them. In particular, it describes and highlights the interest and difficulty in developing chiral simple (small and non-aggregated) organic molecules able to emit left- or right-circularly polarized light efficiently, the efforts realized up to now to reach this challenging objective, and the most significant milestones achieved to date. General guidelines for the preparation of these interesting molecules are also presented. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Non-traditional applications of laser desorption/ionization mass spectrometry

NASA Astrophysics Data System (ADS)

McAlpin, Casey R.

Seven studies were carried out using laser desorption/ionization mass spectrometry (LDI MS) to develop enhanced methodologies for a variety of analyte systems by investigating analyte chemistries, ionization processes, and elimination of spectral interferences. Applications of LDI and matrix assisted laser/desorption/ionization (MALDI) have been previously limited by poorly understood ionization phenomena, and spectral interferences from matrices. Matrix assisted laser desorption ionization MS is well suited to the analysis of proteins. However, the proteins associated with bacteriophages often form complexes which are too massive for detection with a standard MALDI mass spectrometer. As such, methodologies for pretreatment of these samples are discussed in detail in the first chapter. Pretreatment of bacteriophage samples with reducing agents disrupted disulfide linkages and allowed enhanced detection of bacteriophage proteins. The second chapter focuses on the use of MALDI MS for lipid compounds whose molecular mass is significantly less than the proteins for which MALDI is most often applied. The use of MALDI MS for lipid analysis presented unique challenges such as matrix interference and differential ionization efficiencies. It was observed that optimization of the matrix system, and addition of cationization reagents mitigated these challenges and resulted in an enhanced methodology for MALDI MS of lipids. One of the challenges commonly encountered in efforts to expand MALDI MS applications is as previously mentioned interferences introduced by organic matrix molecules. The third chapter focuses on the development of a novel inorganic matrix replacement system called metal oxide laser ionization mass spectrometry (MOLI MS). In contrast to other matrix replacements, considerable effort was devoted to elucidating the ionization mechanism. It was shown that chemisorption of analytes to the metal oxide surface produced acidic adsorbed species which then protonated free analyte molecules. Expanded applications of MOLI MS were developed following description of the ionization mechanism. A series of experiments were carried out involving treatment of metal oxide surfaces with reagent molecules to expand MOLI MS and develop enhanced MOLI MS methodologies. It was found that treatment of the metal oxide surface with a small molecule to act as a proton source expanded MOLI MS to analytes which did not form acidic adsorbed species. Proton-source pretreated MOLI MS was then used for the analysis of oils obtained from the fast, anoxic pyrolysis of biomass (py-oil). These samples are complex and produce MOLI mass spectra with many peaks. In this experiment, methods of data reduction including Kendrick mass defects and nominal mass z*-scores, which are commonly used for the study of petroleum fractions, were used to interpret these spectra and identify the major constituencies of py-oils. Through data reduction and collision induced dissociation (CID), homologous series of compounds were rapidly identified. The final chapter involves using metal oxides to catalytically cleave the ester linkage on lipids containing fatty acids in addition to ionization. The cleavage process results in the production of spectra similar to those observed with saponification/methylation. Fatty acid profiles were generated for a variety of micro-organisms to differentiate between bacterial species. (Abstract shortened by UMI.)

A single Watson-Crick G x C base pair in water: aqueous hydrogen bonds in hydrophobic cavities.

PubMed

Sawada, Tomohisa; Fujita, Makoto

2010-05-26

Hydrogen bond (H-bond) formation in water has been a challenging task because water molecules are constant competitors. In biological systems, however, stable H-bonds are formed by shielding the H-bonding sites from the competing water molecules within hydrophobic pockets. Inspired by the nature's elaborated way, we found that even mononucleotides (G and C) can form the minimal G x C Watson-Crick pair in water by simply providing a synthetic cavity that efficiently shields the Watson-Crick H-bonding sites. The minimal Watson-Crick structure in water was elucidated by NMR study and firmly characterized by crystallographic analysis. The crystal structure also displays that, within the cavity, coencapsulated anions and solvents efficiently mediate the minimal G x C Watson-Crick pair formation. Furthermore, the competition experiments with the other nucleobases clearly revealed the evident selectivity for the G x C base pairing in water. These results show the fact that a H-bonded nucleobase pair was effectively induced and stabilized in the local environment of an artificial hydrophobic cavity.

Single-molecule spectroscopy of LHCSR1 protein dynamics identifies two distinct states responsible for multi-timescale photosynthetic photoprotection

NASA Astrophysics Data System (ADS)

Kondo, Toru; Pinnola, Alberta; Chen, Wei Jia; Dall'Osto, Luca; Bassi, Roberto; Schlau-Cohen, Gabriela S.

2017-08-01

In oxygenic photosynthesis, light harvesting is regulated to safely dissipate excess energy and prevent the formation of harmful photoproducts. Regulation is known to be necessary for fitness, but the molecular mechanisms are not understood. One challenge has been that ensemble experiments average over active and dissipative behaviours, preventing identification of distinct states. Here, we use single-molecule spectroscopy to uncover the photoprotective states and dynamics of the light-harvesting complex stress-related 1 (LHCSR1) protein, which is responsible for dissipation in green algae and moss. We discover the existence of two dissipative states. We find that one of these states is activated by pH and the other by carotenoid composition, and that distinct protein dynamics regulate these states. Together, these two states enable the organism to respond to two types of intermittency in solar intensity—step changes (clouds and shadows) and ramp changes (sunrise), respectively. Our findings reveal key control mechanisms underlying photoprotective dissipation, with implications for increasing biomass yields and developing robust solar energy devices.

Single polymer dynamics under large amplitude oscillatory extension

NASA Astrophysics Data System (ADS)

Zhou, Yuecheng; Schroeder, Charles M.

2016-09-01

Understanding the conformational dynamics of polymers in time-dependent flows is of key importance for controlling materials properties during processing. Despite this importance, however, it has been challenging to study polymer dynamics in controlled time-dependent or oscillatory extensional flows. In this work, we study the dynamics of single polymers in large-amplitude oscillatory extension (LAOE) using a combination of experiments and Brownian dynamics (BD) simulations. Two-dimensional LAOE flow is generated using a feedback-controlled stagnation point device known as the Stokes trap, thereby generating an oscillatory planar extensional flow with alternating principal axes of extension and compression. Our results show that polymers experience periodic cycles of compression, reorientation, and extension in LAOE, and dynamics are generally governed by a dimensionless flow strength (Weissenberg number Wi) and dimensionless frequency (Deborah number De). Single molecule experiments are compared to BD simulations with and without intramolecular hydrodynamic interactions (HI) and excluded volume (EV) interactions, and good agreement is obtained across a range of parameters. Moreover, transient bulk stress in LAOE is determined from simulations using the Kramers relation, which reveals interesting and unique rheological signatures for this time-dependent flow. We further construct a series of single polymer stretch-flow rate curves (defined as single molecule Lissajous curves) as a function of Wi and De, and we observe qualitatively different dynamic signatures (butterfly, bow tie, arch, and line shapes) across the two-dimensional Pipkin space defined by Wi and De. Finally, polymer dynamics spanning from the linear to nonlinear response regimes are interpreted in the context of accumulated fluid strain in LAOE.

Unified description of H-atom-induced chemicurrents and inelastic scattering.

PubMed

Kandratsenka, Alexander; Jiang, Hongyan; Dorenkamp, Yvonne; Janke, Svenja M; Kammler, Marvin; Wodtke, Alec M; Bünermann, Oliver

2018-01-23

The Born-Oppenheimer approximation (BOA) provides the foundation for virtually all computational studies of chemical binding and reactivity, and it is the justification for the widely used "balls and springs" picture of molecules. The BOA assumes that nuclei effectively stand still on the timescale of electronic motion, due to their large masses relative to electrons. This implies electrons never change their energy quantum state. When molecules react, atoms must move, meaning that electrons may become excited in violation of the BOA. Such electronic excitation is clearly seen for: ( i ) Schottky diodes where H adsorption at Ag surfaces produces electrical "chemicurrent;" ( ii ) Au-based metal-insulator-metal (MIM) devices, where chemicurrents arise from H-H surface recombination; and ( iii ) Inelastic energy transfer, where H collisions with Au surfaces show H-atom translation excites the metal's electrons. As part of this work, we report isotopically selective hydrogen/deuterium (H/D) translational inelasticity measurements in collisions with Ag and Au. Together, these experiments provide an opportunity to test new theories that simultaneously describe both nuclear and electronic motion, a standing challenge to the field. Here, we show results of a recently developed first-principles theory that quantitatively explains both inelastic scattering experiments that probe nuclear motion and chemicurrent experiments that probe electronic excitation. The theory explains the magnitude of chemicurrents on Ag Schottky diodes and resolves an apparent paradox--chemicurrents exhibit a much larger isotope effect than does H/D inelastic scattering. It also explains why, unlike Ag-based Schottky diodes, Au-based MIM devices are insensitive to H adsorption.

Multiplexed single-molecule force spectroscopy using a centrifuge.

PubMed

Yang, Darren; Ward, Andrew; Halvorsen, Ken; Wong, Wesley P

2016-03-17

We present a miniature centrifuge force microscope (CFM) that repurposes a benchtop centrifuge for high-throughput single-molecule experiments with high-resolution particle tracking, a large force range, temperature control and simple push-button operation. Incorporating DNA nanoswitches to enable repeated interrogation by force of single molecular pairs, we demonstrate increased throughput, reliability and the ability to characterize population heterogeneity. We perform spatiotemporally multiplexed experiments to collect 1,863 bond rupture statistics from 538 traceable molecular pairs in a single experiment, and show that 2 populations of DNA zippers can be distinguished using per-molecule statistics to reduce noise.

Multiplexed single-molecule force spectroscopy using a centrifuge

PubMed Central

Yang, Darren; Ward, Andrew; Halvorsen, Ken; Wong, Wesley P.

2016-01-01

We present a miniature centrifuge force microscope (CFM) that repurposes a benchtop centrifuge for high-throughput single-molecule experiments with high-resolution particle tracking, a large force range, temperature control and simple push-button operation. Incorporating DNA nanoswitches to enable repeated interrogation by force of single molecular pairs, we demonstrate increased throughput, reliability and the ability to characterize population heterogeneity. We perform spatiotemporally multiplexed experiments to collect 1,863 bond rupture statistics from 538 traceable molecular pairs in a single experiment, and show that 2 populations of DNA zippers can be distinguished using per-molecule statistics to reduce noise. PMID:26984516

Identification and Use of the Putative Bacteroides ovatus Xylanase Promoter for the Inducible Production of Recombinant Human Proteins

USDA-ARS?s Scientific Manuscript database

The use of genetically modified bacteria to deliver biologically active molecules directly to the gut has become an increasingly attractive area of investigation. The challenge of regulation of production of the therapeutic molecule and colonization of the bowel led us to investigate Bacteroides ov...

Photoinduced Oxidative DNA Damage Revealed by an Agarose Gel Nicking Assay: A Biophysical Chemistry Laboratory Experiment

NASA Astrophysics Data System (ADS)

Shafirovich, Vladimir; Singh, Carolyn; Geacintov, Nicholas E.

2003-11-01

Oxidative damage of DNA molecules associated with electron-transfer reactions is an important phenomenon in living cells, which can lead to mutations and contribute to carcinogenesis and the aging processes. This article describes the design of several simple experiments to explore DNA damage initiated by photoinduced electron-transfer reactions sensitized by the acridine derivative, proflavine (PF). A supercoiled DNA agarose gel nicking assay is employed as a sensitive probe of DNA strand cleavage. A low-cost experimental and computer-interfaced imaging apparatus is described allowing for the digital recording and analysis of the gel electrophoresis results. The first experiment describes the formation of direct strand breaks in double-stranded DNA induced by photoexcitation of the intercalated PF molecules. The second experiment demonstrates that the addition of the well-known electron acceptor, methylviologen, gives rise to a significant enhancement of the photochemical DNA strand cleavage effect. This occurs by an electron transfer step to methylviologen that renders the inital photoinduced charge separation between photoexcited PF and DNA irreversible. The third experiment demonstrates that the action spectrum of the DNA photocleavage matches the absorption spectrum of DNA-bound, intercalated PF molecules, which differs from that of free PF molecules. This result demonstrates that the photoinduced DNA strand cleavage is initiated by intercalated rather than free PF molecules.

Conformation-based signal transfer and processing at the single-molecule level

NASA Astrophysics Data System (ADS)

Li, Chao; Wang, Zhongping; Lu, Yan; Liu, Xiaoqing; Wang, Li

2017-11-01

Building electronic components made of individual molecules is a promising strategy for the miniaturization and integration of electronic devices. However, the practical realization of molecular devices and circuits for signal transmission and processing at room temperature has proven challenging. Here, we present room-temperature intermolecular signal transfer and processing using SnCl2Pc molecules on a Cu(100) surface. The in-plane orientations of the molecules are effectively coupled via intermolecular interaction and serve as the information carrier. In the coupled molecular arrays, the signal can be transferred from one molecule to another in the in-plane direction along predesigned routes and processed to realize logical operations. These phenomena enable the use of molecules displaying intrinsic bistable states as complex molecular devices and circuits with novel functions.

The VSEPR Challenge: A Student's Perspective

ERIC Educational Resources Information Center

Jennings, Ashley S.

2010-01-01

To solve the challenge of learning VSEPR molecules in three dimensions, a high school student leverages her passion for 3D computer animation to develop a creative solution. This article outlines the process and story behind the creation of her unique video. (Contains 1 figure.)

Molecular Dynamics Study of the Solution Structure, Clustering, and Diffusion of Four Aqueous Alkanolamines.

PubMed

Melnikov, Sergey M; Stein, Matthias

2018-03-15

CO 2 sequestration from anthropogenic resources is a challenge to the design of environmental processes at a large scale. Reversible chemical absorption by amine-based solvents is one of the most efficient methods of CO 2 removal. Molecular simulation techniques are very useful tools to investigate CO 2 binding by aqueous alkanolamine molecules for further technological application. In the present work, we have performed detailed atomistic molecular dynamics simulations of aqueous solutions of three prototype amines: monoethanolamine (MEA) as a standard, 3-aminopropanol (MPA), 2-methylaminoethanol (MMEA), and 4-diethylamino-2-butanol (DEAB) as potential novel CO 2 absorptive solvents. Solvent densities, radial distribution functions, cluster size distributions, hydrogen-bonding statistics, and diffusion coefficients for a full range of mixture compositions have been obtained. The solvent densities and diffusion coefficients from simulations are in good agreement with those in the experiment. In aqueous solution, MEA, MPA, and MMEA molecules prefer to be fully solvated by water molecules, whereas DEAB molecules tend to self-aggregate. In a range from 30/70-50/50 (w/w) alkanolamine/water mixtures, they form a bicontinuous phase (both alkanolamine and water are organized in two mutually percolating clusters). Among the studied aqueous alkanolamine solutions, the diffusion coefficients decrease in the following order MEA > MPA = MMEA > DEAB. With an increase of water content, the diffusion coefficients increase for all studied alkanolamines. The presented results are a first step for process-scale simulation and provide important qualitative and quantitative information for the design and engineering of efficient new CO 2 removal processes.

Wavefront correction using machine learning methods for single molecule localization microscopy

NASA Astrophysics Data System (ADS)

Tehrani, Kayvan F.; Xu, Jianquan; Kner, Peter

2015-03-01

Optical Aberrations are a major challenge in imaging biological samples. In particular, in single molecule localization (SML) microscopy techniques (STORM, PALM, etc.) a high Strehl ratio point spread function (PSF) is necessary to achieve sub-diffraction resolution. Distortions in the PSF shape directly reduce the resolution of SML microscopy. The system aberrations caused by the imperfections in the optics and instruments can be compensated using Adaptive Optics (AO) techniques prior to imaging. However, aberrations caused by the biological sample, both static and dynamic, have to be dealt with in real time. A challenge for wavefront correction in SML microscopy is a robust optimization approach in the presence of noise because of the naturally high fluctuations in photon emission from single molecules. Here we demonstrate particle swarm optimization for real time correction of the wavefront using an intensity independent metric. We show that the particle swarm algorithm converges faster than the genetic algorithm for bright fluorophores.

Diversity-oriented synthetic strategy for developing a chemical modulator of protein-protein interaction

NASA Astrophysics Data System (ADS)

Kim, Jonghoon; Jung, Jinjoo; Koo, Jaeyoung; Cho, Wansang; Lee, Won Seok; Kim, Chanwoo; Park, Wonwoo; Park, Seung Bum

2016-10-01

Diversity-oriented synthesis (DOS) can provide a collection of diverse and complex drug-like small molecules, which is critical in the development of new chemical probes for biological research of undruggable targets. However, the design and synthesis of small-molecule libraries with improved biological relevance as well as maximized molecular diversity represent a key challenge. Herein, we employ functional group-pairing strategy for the DOS of a chemical library containing privileged substructures, pyrimidodiazepine or pyrimidine moieties, as chemical navigators towards unexplored bioactive chemical space. To validate the utility of this DOS library, we identify a new small-molecule inhibitor of leucyl-tRNA synthetase-RagD protein-protein interaction, which regulates the amino acid-dependent activation of mechanistic target of rapamycin complex 1 signalling pathway. This work highlights that privileged substructure-based DOS strategy can be a powerful research tool for the construction of drug-like compounds to address challenging biological targets.

Column densities resulting from shuttle sublimator/evaporator operation. [optical density of nozzle flow containing water vapor

NASA Technical Reports Server (NTRS)

Naumann, R. J.

1973-01-01

The proposed disposal of H2O from the shuttle fuel cell operation by ejecting it in vapor form through a supersonic nozzle at the rate of 100 lb/day has been investigated from the point of view of the possible interference to astronomical experiments. If the nozzle is located at the tail and directed along the shuttle longitudinal axis, the resulting column density will be less than 10 to th 12th power molecules/sq cm at viewing angles larger than 48 deg above the longitudinal axis. The molecules in the trail will diffuse rapidly. The column density contribution from molecules expelled on the previous orbit is 1.3 x 10 to the 8th power molecules/sq cm. This contribution diminishes by the inverse square root of the number of orbits since the molecules were expelled. The molecular backscatter from atmospheric molecules is also calculated. If the plume is directed into the flight path, the column density along a perpendicular is found to be 1.5 x 10 to the 11th power molecules/sq cm. The return flux is estimated to be of the order of 10 to the 12th power molecules/sq cm/sec at the stagnation point. With reasonable care in design of experiments to protect them from the backscatter flux of water molecules, the expulsion of 100 lb/day does not appear to create an insurmountable difficulty for the shuttle experiments.

Decay behaviors of the Pc hadronic molecules

NASA Astrophysics Data System (ADS)

Lin, Yong-Hui; Shen, Chao-Wei; Guo, Feng-Kun; Zou, Bing-Song

2017-06-01

The Pc(4380 ) and Pc(4450 ) states observed recently by the LHCb experiment were proposed to be either D ¯Σc* or D¯*Σc bound states. We analyze the decay behaviors of two such types of hadronic molecules within the effective Lagrangian framework. With branching ratios of ten possible decay channels calculated, it is found that the two types of hadronic molecules have distinguishable decay patterns. While the D ¯Σc* molecule decays dominantly to the D¯*Λc channel with a branching ratio by 2 orders of magnitude larger than to D ¯Λc, the D¯*Σc molecule decays to these two channels with a difference of less than a factor of 2. Our results show that the total decay width of Pc(4380 ) as the spin-parity-3/2- D ¯Σc* molecule is about a factor of 2 larger than the corresponding value for the D¯*Σc molecule. It suggests that the assignment of the D ¯Σc* molecule for Pc(4380 ) is more favorable than the D¯*Σc molecule. In addition, Pc(4450 ) seems to be a D¯*Σc molecule with JP=5/2+ in our scheme. Based on these partial decay widths of the Pc states, we estimate the cross sections for the reactions γ p →J /ψ p and π p →J /ψ p through the s-channel Pc states. The forthcoming γ p experiment at JLAB and the π p experiment at JPARC should be able to pin down the nature of these Pc states.

Real-time single-molecule imaging of quantum interference.

PubMed

Juffmann, Thomas; Milic, Adriana; Müllneritsch, Michael; Asenbaum, Peter; Tsukernik, Alexander; Tüxen, Jens; Mayor, Marcel; Cheshnovsky, Ori; Arndt, Markus

2012-03-25

The observation of interference patterns in double-slit experiments with massive particles is generally regarded as the ultimate demonstration of the quantum nature of these objects. Such matter-wave interference has been observed for electrons, neutrons, atoms and molecules and, in contrast to classical physics, quantum interference can be observed when single particles arrive at the detector one by one. The build-up of such patterns in experiments with electrons has been described as the "most beautiful experiment in physics". Here, we show how a combination of nanofabrication and nano-imaging allows us to record the full two-dimensional build-up of quantum interference patterns in real time for phthalocyanine molecules and for derivatives of phthalocyanine molecules, which have masses of 514 AMU and 1,298 AMU respectively. A laser-controlled micro-evaporation source was used to produce a beam of molecules with the required intensity and coherence, and the gratings were machined in 10-nm-thick silicon nitride membranes to reduce the effect of van der Waals forces. Wide-field fluorescence microscopy detected the position of each molecule with an accuracy of 10 nm and revealed the build-up of a deterministic ensemble interference pattern from single molecules that arrived stochastically at the detector. In addition to providing this particularly clear demonstration of wave-particle duality, our approach could also be used to study larger molecules and explore the boundary between quantum and classical physics.

Real-time single-molecule imaging of quantum interference

NASA Astrophysics Data System (ADS)

Juffmann, Thomas; Milic, Adriana; Müllneritsch, Michael; Asenbaum, Peter; Tsukernik, Alexander; Tüxen, Jens; Mayor, Marcel; Cheshnovsky, Ori; Arndt, Markus

2012-05-01

The observation of interference patterns in double-slit experiments with massive particles is generally regarded as the ultimate demonstration of the quantum nature of these objects. Such matter-wave interference has been observed for electrons, neutrons, atoms and molecules and, in contrast to classical physics, quantum interference can be observed when single particles arrive at the detector one by one. The build-up of such patterns in experiments with electrons has been described as the ``most beautiful experiment in physics''. Here, we show how a combination of nanofabrication and nano-imaging allows us to record the full two-dimensional build-up of quantum interference patterns in real time for phthalocyanine molecules and for derivatives of phthalocyanine molecules, which have masses of 514 AMU and 1,298 AMU respectively. A laser-controlled micro-evaporation source was used to produce a beam of molecules with the required intensity and coherence, and the gratings were machined in 10-nm-thick silicon nitride membranes to reduce the effect of van der Waals forces. Wide-field fluorescence microscopy detected the position of each molecule with an accuracy of 10 nm and revealed the build-up of a deterministic ensemble interference pattern from single molecules that arrived stochastically at the detector. In addition to providing this particularly clear demonstration of wave-particle duality, our approach could also be used to study larger molecules and explore the boundary between quantum and classical physics.

Discerning the Location and Nature of Coke Deposition from Surface to Bulk of Spent Zeolite Catalysts

NASA Astrophysics Data System (ADS)

Devaraj, Arun; Vijayakumar, Murugesan; Bao, Jie; Guo, Mond F.; Derewinski, Miroslaw A.; Xu, Zhijie; Gray, Michel J.; Prodinger, Sebastian; Ramasamy, Karthikeyan K.

2016-11-01

The formation of carbonaceous deposits (coke) in zeolite pores during catalysis leads to temporary deactivation of catalyst, necessitating regeneration steps, affecting throughput, and resulting in partial permanent loss of catalytic efficiency. Yet, even to date, the coke molecule distribution is quite challenging to study with high spatial resolution from surface to bulk of the catalyst particles at a single particle level. To address this challenge we investigated the coke molecules in HZSM-5 catalyst after ethanol conversion treatment by a combination of C K-edge X-ray absorption spectroscopy (XAS), 13C Cross polarization-magic angle spinning nuclear magnetic resonance (CP-MAS NMR) spectroscopy, and atom probe tomography (APT). XAS and NMR highlighted the aromatic character of coke molecules. APT permitted the imaging of the spatial distribution of hydrocarbon molecules located within the pores of spent HZSM-5 catalyst from surface to bulk at a single particle level. 27Al NMR results and APT results indicated association of coke molecules with Al enriched regions within the spent HZSM-5 catalyst particles. The experimental results were additionally validated by a level-set-based APT field evaporation model. These results provide a new approach to investigate catalytic deactivation due to hydrocarbon coking or poisoning of zeolites at an unprecedented spatial resolution.

Discerning the Location and Nature of Coke Deposition from Surface to Bulk of Spent Zeolite Catalysts

PubMed Central

Devaraj, Arun; Vijayakumar, Murugesan; Bao, Jie; Guo, Mond F.; Derewinski, Miroslaw A.; Xu, Zhijie; Gray, Michel J.; Prodinger, Sebastian; Ramasamy, Karthikeyan K.

2016-01-01

The formation of carbonaceous deposits (coke) in zeolite pores during catalysis leads to temporary deactivation of catalyst, necessitating regeneration steps, affecting throughput, and resulting in partial permanent loss of catalytic efficiency. Yet, even to date, the coke molecule distribution is quite challenging to study with high spatial resolution from surface to bulk of the catalyst particles at a single particle level. To address this challenge we investigated the coke molecules in HZSM-5 catalyst after ethanol conversion treatment by a combination of C K-edge X-ray absorption spectroscopy (XAS), 13C Cross polarization-magic angle spinning nuclear magnetic resonance (CP-MAS NMR) spectroscopy, and atom probe tomography (APT). XAS and NMR highlighted the aromatic character of coke molecules. APT permitted the imaging of the spatial distribution of hydrocarbon molecules located within the pores of spent HZSM-5 catalyst from surface to bulk at a single particle level. 27Al NMR results and APT results indicated association of coke molecules with Al enriched regions within the spent HZSM-5 catalyst particles. The experimental results were additionally validated by a level-set–based APT field evaporation model. These results provide a new approach to investigate catalytic deactivation due to hydrocarbon coking or poisoning of zeolites at an unprecedented spatial resolution. PMID:27876869

A wireless centrifuge force microscope (CFM) enables multiplexed single-molecule experiments in a commercial centrifuge.

PubMed

Hoang, Tony; Patel, Dhruv S; Halvorsen, Ken

2016-08-01

The centrifuge force microscope (CFM) was recently introduced as a platform for massively parallel single-molecule manipulation and analysis. Here we developed a low-cost and self-contained CFM module that works directly within a commercial centrifuge, greatly improving accessibility and ease of use. Our instrument incorporates research grade video microscopy, a power source, a computer, and wireless transmission capability to simultaneously monitor many individually tethered microspheres. We validated the instrument by performing single-molecule force shearing of short DNA duplexes. For a 7 bp duplex, we observed over 1000 dissociation events due to force dependent shearing from 2 pN to 12 pN with dissociation times in the range of 10-100 s. We extended the measurement to a 10 bp duplex, applying a 12 pN force clamp and directly observing single-molecule dissociation over an 85 min experiment. Our new CFM module facilitates simple and inexpensive experiments that dramatically improve access to single-molecule analysis.

An approach to spin-resolved molecular gas microscopy

NASA Astrophysics Data System (ADS)

Covey, Jacob P.; De Marco, Luigi; Acevedo, Óscar L.; Rey, Ana Maria; Ye, Jun

2018-04-01

Ultracold polar molecules are an ideal platform for studying many-body physics with long-range dipolar interactions. Experiments in this field have progressed enormously, and several groups are pursuing advanced apparatus for manipulation of molecules with electric fields as well as single-atom-resolved in situ detection. Such detection has become ubiquitous for atoms in optical lattices and tweezer arrays, but has yet to be demonstrated for ultracold polar molecules. Here we present a proposal for the implementation of site-resolved microscopy for polar molecules, and specifically discuss a technique for spin-resolved molecular detection. We use numerical simulation of spin dynamics of lattice-confined polar molecules to show how such a scheme would be of utility in a spin-diffusion experiment.

Digital encoding of cellular mRNAs enabling precise and absolute gene expression measurement by single-molecule counting.

PubMed

Fu, Glenn K; Wilhelmy, Julie; Stern, David; Fan, H Christina; Fodor, Stephen P A

2014-03-18

We present a new approach for the sensitive detection and accurate quantitation of messenger ribonucleic acid (mRNA) gene transcripts in single cells. First, the entire population of mRNAs is encoded with molecular barcodes during reverse transcription. After amplification of the gene targets of interest, molecular barcodes are counted by sequencing or scored on a simple hybridization detector to reveal the number of molecules in the starting sample. Since absolute quantities are measured, calibration to standards is unnecessary, and many of the relative quantitation challenges such as polymerase chain reaction (PCR) bias are avoided. We apply the method to gene expression analysis of minute sample quantities and demonstrate precise measurements with sensitivity down to sub single-cell levels. The method is an easy, single-tube, end point assay utilizing standard thermal cyclers and PCR reagents. Accurate and precise measurements are obtained without any need for cycle-to-cycle intensity-based real-time monitoring or physical partitioning into multiple reactions (e.g., digital PCR). Further, since all mRNA molecules are encoded with molecular barcodes, amplification can be used to generate more material for multiple measurements and technical replicates can be carried out on limited samples. The method is particularly useful for small sample quantities, such as single-cell experiments. Digital encoding of cellular content preserves true abundance levels and overcomes distortions introduced by amplification.

Adsorption of Organic Molecules to van der Waals Materials: Comparison of Fluorographene and Fluorographite with Graphene and Graphite

PubMed Central

2017-01-01

Understanding strength and nature of noncovalent binding to surfaces imposes significant challenge both for computations and experiments. We explored the adsorption of five small nonpolar organic molecules (acetone, acetonitrile, dichloromethane, ethanol, ethyl acetate) to fluorographene and fluorographite using inverse gas chromatography and theoretical calculations, providing new insights into the strength and nature of adsorption of small organic molecules on these surfaces. The measured adsorption enthalpies on fluorographite range from −7 to −13 kcal/mol and are by 1–2 kcal/mol lower than those measured on graphene/graphite, which indicates higher affinity of organic adsorbates to fluorographene than to graphene. The dispersion-corrected functionals performed well, and the nonlocal vdW DFT functionals (particularly optB86b-vdW) achieved the best agreement with the experimental data. Computations show that the adsorption enthalpies are controlled by the interaction energy, which is dominated by London dispersion forces (∼70%). The calculations also show that bonding to structural features, like edges and steps, as well as defects does not significantly increase the adsorption enthalpies, which explains a low sensitivity of measured adsorption enthalpies to coverage. The adopted Langmuir model for fitting experimental data enabled determination of adsorption entropies. The adsorption on the fluorographene/fluorographite surface resulted in an entropy loss equal to approximately 40% of the gas phase entropy. PMID:28145699

Noise reduction in single time frame optical DNA maps

PubMed Central

Müller, Vilhelm; Westerlund, Fredrik

2017-01-01

In optical DNA mapping technologies sequence-specific intensity variations (DNA barcodes) along stretched and stained DNA molecules are produced. These “fingerprints” of the underlying DNA sequence have a resolution of the order one kilobasepairs and the stretching of the DNA molecules are performed by surface adsorption or nano-channel setups. A post-processing challenge for nano-channel based methods, due to local and global random movement of the DNA molecule during imaging, is how to align different time frames in order to produce reproducible time-averaged DNA barcodes. The current solutions to this challenge are computationally rather slow. With high-throughput applications in mind, we here introduce a parameter-free method for filtering a single time frame noisy barcode (snap-shot optical map), measured in a fraction of a second. By using only a single time frame barcode we circumvent the need for post-processing alignment. We demonstrate that our method is successful at providing filtered barcodes which are less noisy and more similar to time averaged barcodes. The method is based on the application of a low-pass filter on a single noisy barcode using the width of the Point Spread Function of the system as a unique, and known, filtering parameter. We find that after applying our method, the Pearson correlation coefficient (a real number in the range from -1 to 1) between the single time-frame barcode and the time average of the aligned kymograph increases significantly, roughly by 0.2 on average. By comparing to a database of more than 3000 theoretical plasmid barcodes we show that the capabilities to identify plasmids is improved by filtering single time-frame barcodes compared to the unfiltered analogues. Since snap-shot experiments and computational time using our method both are less than a second, this study opens up for high throughput optical DNA mapping with improved reproducibility. PMID:28640821

A quantum spin-probe molecular microscope

NASA Astrophysics Data System (ADS)

Perunicic, V. S.; Hill, C. D.; Hall, L. T.; Hollenberg, L. C. L.

2016-10-01

Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy.

Native and Reconstituted Plasma Lipoproteins in Nanomedicine: Physicochemical Determinants of Nanoparticle Structure, Stability, and Metabolism

PubMed Central

Pownall, Henry J.; Rosales, Corina; Gillard, Baiba K.; Ferrari, Mauro

2016-01-01

Although many acute and chronic diseases are managed via pharmacological means, challenges remain regarding appropriate drug targeting and maintenance of therapeutic levels within target tissues. Advances in nanotechnology will overcome these challenges through the development of lipidic particles, including liposomes, lipoproteins, and reconstituted high-density lipoproteins (rHDL) that are potential carriers of water-soluble, hydrophobic, and amphiphilic molecules. Herein we summarize the properties of human plasma lipoproteins and rHDL, identify the physicochemical determinants of lipid transfer between phospholipid surfaces, and discuss strategies for increasing the plasma half-life of lipoprotein- and liposome-associated molecules. PMID:27826368

From Vesicles to Protocells: The Roles of Amphiphilic Molecules

PubMed Central

Sakuma, Yuka; Imai, Masayuki

2015-01-01

It is very challenging to construct protocells from molecular assemblies. An important step in this challenge is the achievement of vesicle dynamics that are relevant to cellular functions, such as membrane trafficking and self-reproduction, using amphiphilic molecules. Soft matter physics will play an important role in the development of vesicles that have these functions. Here, we show that simple binary phospholipid vesicles have the potential to reproduce the relevant functions of adhesion, pore formation and self-reproduction of vesicles, by coupling the lipid geometries (spontaneous curvatures) and the phase separation. This achievement will elucidate the pathway from molecular assembly to cellular life. PMID:25738256

Molecules to maps: tools for visualization and interaction in support of computational biology.

PubMed

Kraemer, E T; Ferrin, T E

1998-01-01

The volume of data produced by genome projects, X-ray crystallography, NMR spectroscopy, and electron and confocal microscopy present the bioinformatics community with new challenges for analyzing, understanding, and exchanging this data. At the 1998 Pacific Symposium on Biocomputing, a track entitled 'Molecules to Maps: Tools for Visualization and Interaction in Computational Biology' provided tool developers and users with the opportunity to discuss advances in tools and techniques to assist scientists in evaluating, absorbing, navigating, and correlating this sea of information, through visualization and user interaction. In this paper we present these advances and discuss some of the challenges that remain to be solved.

Resveratrol Photoisomerization: An Integrative Guided-Inquiry Experiment

ERIC Educational Resources Information Center

Bernanrd, Elyse; Britz-McKibbin, Philip; Gernigon, Nicholas

2007-01-01

The recently introduced integrative guided-inquiry experiment explains various fundamental chemical concepts related to different biologically relevant molecules like resveratrol. The results of the photoisomerization of the molecule show that it is a very effective chemopreventative agent that can extend the lifespan in several organisms.

Exchange and correlation in positronium-molecule scattering

NASA Astrophysics Data System (ADS)

Fabrikant, I. I.; Wilde, R. S.

2018-05-01

Exchange and correlations play a particularly important role in positronium (Ps) collisions with atoms and molecules, since the static potential for Ps interaction with a neutral system is zero. Theoretical description of both effects is a very challenging task. In the present work we use the free-electron-gas model to describe exchange and correlations in Ps collisions with molecules similar to the approach widely used in the theory of electron-molecule collisions. The results for exchange and correlation energies are presented as functions of the Fermi momentum of the electron gas and the Ps incident energy. Using the Thomas-Fermi model, these functions can be converted into exchange and correlation potentials for Ps interaction with molecules as functions of the distance between the projectile and the target.

Xylan-regulated Delivery of Human Keratinocyte Growth Factor-2 to the Inflamed Colon by the Human Anaerobic Commensal Bacterium Bacteroides ovatus

USDA-ARS?s Scientific Manuscript database

The use of genetically modified bacteria to deliver biologically active molecules directly to the gut has become an increasingly attractive area of investigation. The challenge of regulation of production of the therapeutic molecule and colonization of the bowel led us to investigate Bacteroides ov...

Analyzing Single-Molecule Time Series via Nonparametric Bayesian Inference

PubMed Central

Hines, Keegan E.; Bankston, John R.; Aldrich, Richard W.

2015-01-01

The ability to measure the properties of proteins at the single-molecule level offers an unparalleled glimpse into biological systems at the molecular scale. The interpretation of single-molecule time series has often been rooted in statistical mechanics and the theory of Markov processes. While existing analysis methods have been useful, they are not without significant limitations including problems of model selection and parameter nonidentifiability. To address these challenges, we introduce the use of nonparametric Bayesian inference for the analysis of single-molecule time series. These methods provide a flexible way to extract structure from data instead of assuming models beforehand. We demonstrate these methods with applications to several diverse settings in single-molecule biophysics. This approach provides a well-constrained and rigorously grounded method for determining the number of biophysical states underlying single-molecule data. PMID:25650922

Cell-targetable DNA nanocapsules for spatiotemporal release of caged bioactive small molecules

NASA Astrophysics Data System (ADS)

Veetil, Aneesh T.; Chakraborty, Kasturi; Xiao, Kangni; Minter, Myles R.; Sisodia, Sangram S.; Krishnan, Yamuna

2017-12-01

Achieving triggered release of small molecules with spatial and temporal precision at designated cells within an organism remains a challenge. By combining a cell-targetable, icosahedral DNA-nanocapsule loaded with photoresponsive polymers, we show cytosolic delivery of small molecules with the spatial resolution of single endosomes in specific cells in Caenorhabditis elegans. Our technology can report on the extent of small molecules released after photoactivation as well as pinpoint the location at which uncaging of the molecules occurred. We apply this technology to release dehydroepiandrosterone (DHEA), a neurosteroid that promotes neurogenesis and neuron survival, and determined the timescale of neuronal activation by DHEA, using light-induced release of DHEA from targeted DNA nanocapsules. Importantly, sequestration inside the DNA capsule prevents photocaged DHEA from activating neurons prematurely. Our methodology can in principle be generalized to diverse neurostimulatory molecules.

Motor-motor interactions in ensembles of muscle myosin: using theory to connect single molecule to ensemble measurements

NASA Astrophysics Data System (ADS)

Walcott, Sam

2013-03-01

Interactions between the proteins actin and myosin drive muscle contraction. Properties of a single myosin interacting with an actin filament are largely known, but a trillion myosins work together in muscle. We are interested in how single-molecule properties relate to ensemble function. Myosin's reaction rates depend on force, so ensemble models keep track of both molecular state and force on each molecule. These models make subtle predictions, e.g. that myosin, when part of an ensemble, moves actin faster than when isolated. This acceleration arises because forces between molecules speed reaction kinetics. Experiments support this prediction and allow parameter estimates. A model based on this analysis describes experiments from single molecule to ensemble. In vivo, actin is regulated by proteins that, when present, cause the binding of one myosin to speed the binding of its neighbors; binding becomes cooperative. Although such interactions preclude the mean field approximation, a set of linear ODEs describes these ensembles under simplified experimental conditions. In these experiments cooperativity is strong, with the binding of one molecule affecting ten neighbors on either side. We progress toward a description of myosin ensembles under physiological conditions.

Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test

PubMed Central

Bardwell, David A.; Adjiman, Claire S.; Arnautova, Yelena A.; Bartashevich, Ekaterina; Boerrigter, Stephan X. M.; Braun, Doris E.; Cruz-Cabeza, Aurora J.; Day, Graeme M.; Della Valle, Raffaele G.; Desiraju, Gautam R.; van Eijck, Bouke P.; Facelli, Julio C.; Ferraro, Marta B.; Grillo, Damian; Habgood, Matthew; Hofmann, Detlef W. M.; Hofmann, Fridolin; Jose, K. V. Jovan; Karamertzanis, Panagiotis G.; Kazantsev, Andrei V.; Kendrick, John; Kuleshova, Liudmila N.; Leusen, Frank J. J.; Maleev, Andrey V.; Misquitta, Alston J.; Mohamed, Sharmarke; Needs, Richard J.; Neumann, Marcus A.; Nikylov, Denis; Orendt, Anita M.; Pal, Rumpa; Pantelides, Constantinos C.; Pickard, Chris J.; Price, Louise S.; Price, Sarah L.; Scheraga, Harold A.; van de Streek, Jacco; Thakur, Tejender S.; Tiwari, Siddharth; Venuti, Elisabetta; Zhitkov, Ilia K.

2011-01-01

Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories – a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome. PMID:22101543

Detectors in Extreme Conditions

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

Blaj, G.; Carini, G.; Carron, S.

2015-08-06

Free Electron Lasers opened a new window on imaging the motion of atoms and molecules. At SLAC, FEL experiments are performed at LCLS using 120Hz pulses with 10 12 - 10 13 photons in 10 femtoseconds (billions of times brighter than the most powerful synchrotrons). This extreme detection environment raises unique challenges, from obvious to surprising. Radiation damage is a constant threat due to accidental exposure to insufficiently attenuated beam, focused beam and formation of ice crystals reflecting the beam onto the detector. Often high power optical lasers are also used (e.g., 25TW), increasing the risk of damage or impedingmore » data acquisition through electromagnetic pulses (EMP). The sample can contaminate the detector surface or even produce shrapnel damage. Some experiments require ultra high vacuum (UHV) with strict design, surface contamination and cooling requirements - also for detectors. The setup is often changed between or during experiments with short turnaround times, risking mechanical and ESD damage, requiring work planning, training of operators and sometimes continuous participation of the LCLS Detector Group in the experiments. The detectors used most often at LCLS are CSPAD cameras for hard x-rays and pnCCDs for soft x-rays.« less

Salinity Effects on the Adsorption of Nucleic Acid Compounds on Na-Montmorillonite: a Prebiotic Chemistry Experiment

NASA Astrophysics Data System (ADS)

Villafañe-Barajas, Saúl A.; Baú, João Paulo T.; Colín-García, María; Negrón-Mendoza, Alicia; Heredia-Barbero, Alejandro; Pi-Puig, Teresa; Zaia, Dimas A. M.

2018-02-01

Any proposed model of Earth's primitive environments requires a combination of geochemical variables. Many experiments are prepared in aqueous solutions and in the presence of minerals. However, most sorption experiments are performed in distilled water, and just a few in seawater analogues, mostly inconsistent with a representative primitive ocean model. Therefore, it is necessary to perform experiments that consider the composition and concentration of dissolved salts in the early ocean to understand how these variables could have affected the absorption of organic molecules into minerals. In this work, the adsorption of adenine, adenosine, and 5'AMP onto Na+montmorillonite was studied using a primitive ocean analog (4.0 Ga) from experimental and computational approaches. The order of sorption of the molecules was: 5'AMP > adenine > adenosine. Infrared spectra showed that the interaction between these molecules and montmorillonite occurs through the NH2 group. In addition, electrostatic interaction between negatively charged montmorillonite and positively charge N1 of these molecules could occur. Results indicate that dissolved salts affect the sorption in all cases; the size and structure of each organic molecule influence the amount sorbed. Specifically, the X-ray diffraction patterns show that dissolved salts occupy the interlayer space in Na-montmorillonite and compete with organic molecules for available sites. The adsorption capacity is clearly affected by dissolved salts in thermodynamic terms as deduced by isotherm models. Indeed, molecular dynamic models suggest that salts are absorbed in the interlamellar space and can interact with oxygen atoms exposed in the edges of clay or in its surface, reducing the sorption of the organic molecules. This research shows that the sorption process could be affected by high concentration of salts, since ions and organic molecules may compete for available sites on inorganic surfaces. Salt concentration in primitive oceans may have strongly affected the sorption, and hence the concentration processes of organic molecules on minerals.

Bacillus subtilis spreads by surfing on waves of surfactant

PubMed Central

Angelini, Thomas E.; Roper, Marcus; Kolter, Roberto; Weitz, David A.; Brenner, Michael P.

2009-01-01

The bacterium Bacillus subtilis produces the molecule surfactin, which is known to enhance the spreading of multicellular colonies on nutrient substrates by lowering the surface tension of the surrounding fluid, and to aid in the formation of aerial structures. Here we present experiments and a mathematical model that demonstrate how the differential accumulation rates induced by the geometry of the bacterial film give rise to surfactant waves. The spreading flux increases with increasing biofilm viscosity. Community associations are known to protect bacterial populations from environmental challenges such as predation, heat, or chemical stresses, and enable digestion of a broader range of nutritive sources. This study provides evidence of enhanced dispersal through cooperative motility, and points to nonintuitive methods for controlling the spread of biofilms. PMID:19826092

Metabolomics: A Primer.

PubMed

Liu, Xiaojing; Locasale, Jason W

2017-04-01

Metabolomics generates a profile of small molecules that are derived from cellular metabolism and can directly reflect the outcome of complex networks of biochemical reactions, thus providing insights into multiple aspects of cellular physiology. Technological advances have enabled rapid and increasingly expansive data acquisition with samples as small as single cells; however, substantial challenges in the field remain. In this primer we provide an overview of metabolomics, especially mass spectrometry (MS)-based metabolomics, which uses liquid chromatography (LC) for separation, and discuss its utilities and limitations. We identify and discuss several areas at the frontier of metabolomics. Our goal is to give the reader a sense of what might be accomplished when conducting a metabolomics experiment, now and in the near future. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nitric oxide: cancer target or anticancer agent?

PubMed

Mocellin, Simone

2009-03-01

Despite the improved understanding of nitric oxide (NO) biology and the large amount of preclinical experiments testing its role in cancer development and progression, it is still debated whether NO should be considered a potential anticancer agent or instead a carcinogen. The complexity of NO effects within a cell and the variability of the final biological outcome depending upon NO levels makes it highly challenging to determine the therapeutic value of interfering with the activity of this intriguing gaseous messenger. This uncertainty has so far halted the clinical implementation of NO-based therapeutics in the field of oncology. Accordingly, only an in depth knowledge of the mechanisms leading to experimental tumor regression or progression in response to NO will allow us to exploit this molecule to fight cancer.

Development of a subunit vaccine for infectious pancreatic necrosis virus using a baculovirus insect/larvae system

USGS Publications Warehouse

Shivappa, R.B.; McAllister, P.E.; Edwards, G.H.; Santi, N.; Evensen, O.; Vakharia, V.N.; ,

2005-01-01

Various attempts to develop a vaccine against infectious pancreatic necrosis virus (IPNV) have not yielded consistent results. Thus, at present, no commercial vaccine is available that can be used with confidence to immunize fry of salmon and trout. We generated a cDNA clone of the large genome segment A of an IPNV Sp strain and expressed all structural protein genes in insect cells and larvae using a baculovirus expression system. Green fluorescent protein was also co-expressed as a reporter molecule. High yields of IPNV proteins were obtained and the structural proteins self assembled to form virus-like particles (VLPs). We tested the immunogenicity of the putative VLP antigen in immersion vaccine experiments (two concentrations) in rainbow trout (Oncorhynchus mykiss) fry, and by intraperitoneal immunisation of Atlantic salmon (Salmo salar) pre-smolts using an oil adjuvant formulation. Rainbow trout were challenged by immersion using either the Sp or the VR-299 strain of IPNV two or three weeks post-vaccination, while Atlantic salmon were bath challenged with Sp strain after two months, after parr-smolt transformation. In the rainbow trout fry challenged two weeks post-immunization, cumulative mortality rates three weeks post challenge were 14 % in the fry that had received the highest dose versus 8 % in the control groups. No indication of protection was seen in repeated trials using a lower dose of antigen and challenge three weeks post-immunisation. The cumulative mortality rate of intraperitoneally immunised Atlantic salmon post-smolts four weeks post challenge was lower (56 %) than in the control fish (77 %), showing a dose-response pattern.

Murine Efficacy and Pharmacokinetic Evaluation of the Flaviviral NS5 Capping Enzyme 2-Thioxothiazolidin-4-One Inhibitor BG-323

PubMed Central

Bullard, Kristen M.; Gullberg, Rebekah C.; Soltani, Elnaz; Steel, J. Jordan; Geiss, Brian J.; Keenan, Susan M.

2015-01-01

Arthropod-borne flavivirus infection continues to cause significant morbidity and mortality worldwide. Identification of drug targets and novel antiflaviviral compounds to treat these diseases has become a global health imperative. A previous screen of 235,456 commercially available small molecules identified the 2-thioxothiazolidin-4-one family of compounds as inhibitors of the flaviviral NS5 capping enzyme, a promising target for antiviral drug development. Rational drug design methodologies enabled identification of lead compound BG-323 from this series. We have shown previously that BG-323 potently inhibits NS5 capping enzyme activity, displays antiviral effects in dengue virus replicon assays and inhibits growth of West Nile and yellow fever viruses with low cytotoxicity in vitro. In this study we further characterized BG-323’s antiviral activity in vitro and in vivo. We found that BG-323 was able to reduce replication of WNV (NY99) and Powassan viruses in culture, and we were unable to force resistance into WNV (Kunjin) in long-term culture experiments. We then evaluated the antiviral activity of BG-323 in a murine model. Mice were challenged with WNV NY99 and administered BG-323 or mock by IP inoculation immediately post challenge and twice daily thereafter. Mice were bled and viremia was quantified on day three. No significant differences in viremia were observed between BG-323-treated and control groups and clinical scores indicated both BG-323-treated and control mice developed signs of illness on approximately the same day post challenge. To determine whether differences in in vitro and in vivo efficacy were due to unfavorable pharmacokinetic properties of BG-323, we conducted a pharmacokinetic evaluation of this small molecule. Insights from pharmacokinetic studies indicate that BG-323 is cell permeable, has a low efflux ratio and does not significantly inhibit two common cytochrome P450 (CYP P450) isoforms thus suggesting this molecule may be less likely to cause adverse drug interactions. However, the T1/2 of BG-323 was suboptimal and the percent of drug bound to plasma binding proteins was high. Future studies with BG-323 will be aimed at increasing the T1/2 and determining strategies for mitigating the effects of high plasma protein binding, which likely contribute to low in vivo efficacy. PMID:26075394

Murine Efficacy and Pharmacokinetic Evaluation of the Flaviviral NS5 Capping Enzyme 2-Thioxothiazolidin-4-One Inhibitor BG-323.

PubMed

Bullard, Kristen M; Gullberg, Rebekah C; Soltani, Elnaz; Steel, J Jordan; Geiss, Brian J; Keenan, Susan M

2015-01-01

Arthropod-borne flavivirus infection continues to cause significant morbidity and mortality worldwide. Identification of drug targets and novel antiflaviviral compounds to treat these diseases has become a global health imperative. A previous screen of 235,456 commercially available small molecules identified the 2-thioxothiazolidin-4-one family of compounds as inhibitors of the flaviviral NS5 capping enzyme, a promising target for antiviral drug development. Rational drug design methodologies enabled identification of lead compound BG-323 from this series. We have shown previously that BG-323 potently inhibits NS5 capping enzyme activity, displays antiviral effects in dengue virus replicon assays and inhibits growth of West Nile and yellow fever viruses with low cytotoxicity in vitro. In this study we further characterized BG-323's antiviral activity in vitro and in vivo. We found that BG-323 was able to reduce replication of WNV (NY99) and Powassan viruses in culture, and we were unable to force resistance into WNV (Kunjin) in long-term culture experiments. We then evaluated the antiviral activity of BG-323 in a murine model. Mice were challenged with WNV NY99 and administered BG-323 or mock by IP inoculation immediately post challenge and twice daily thereafter. Mice were bled and viremia was quantified on day three. No significant differences in viremia were observed between BG-323-treated and control groups and clinical scores indicated both BG-323-treated and control mice developed signs of illness on approximately the same day post challenge. To determine whether differences in in vitro and in vivo efficacy were due to unfavorable pharmacokinetic properties of BG-323, we conducted a pharmacokinetic evaluation of this small molecule. Insights from pharmacokinetic studies indicate that BG-323 is cell permeable, has a low efflux ratio and does not significantly inhibit two common cytochrome P450 (CYP P450) isoforms thus suggesting this molecule may be less likely to cause adverse drug interactions. However, the T1/2 of BG-323 was suboptimal and the percent of drug bound to plasma binding proteins was high. Future studies with BG-323 will be aimed at increasing the T1/2 and determining strategies for mitigating the effects of high plasma protein binding, which likely contribute to low in vivo efficacy.

Molecular Modeling of Water Interfaces: From Molecular Spectroscopy to Thermodynamics.

PubMed

Nagata, Yuki; Ohto, Tatsuhiko; Backus, Ellen H G; Bonn, Mischa

2016-04-28

Understanding aqueous interfaces at the molecular level is not only fundamentally important, but also highly relevant for a variety of disciplines. For instance, electrode-water interfaces are relevant for electrochemistry, as are mineral-water interfaces for geochemistry and air-water interfaces for environmental chemistry; water-lipid interfaces constitute the boundaries of the cell membrane, and are thus relevant for biochemistry. One of the major challenges in these fields is to link macroscopic properties such as interfacial reactivity, solubility, and permeability as well as macroscopic thermodynamic and spectroscopic observables to the structure, structural changes, and dynamics of molecules at these interfaces. Simulations, by themselves, or in conjunction with appropriate experiments, can provide such molecular-level insights into aqueous interfaces. In this contribution, we review the current state-of-the-art of three levels of molecular dynamics (MD) simulation: ab initio, force field, and coarse-grained. We discuss the advantages, the potential, and the limitations of each approach for studying aqueous interfaces, by assessing computations of the sum-frequency generation spectra and surface tension. The comparison of experimental and simulation data provides information on the challenges of future MD simulations, such as improving the force field models and the van der Waals corrections in ab initio MD simulations. Once good agreement between experimental observables and simulation can be established, the simulation can be used to provide insights into the processes at a level of detail that is generally inaccessible to experiments. As an example we discuss the mechanism of the evaporation of water. We finish by presenting an outlook outlining four future challenges for molecular dynamics simulations of aqueous interfacial systems.

Single-molecule detection: applications to ultrasensitive biochemical analysis

NASA Astrophysics Data System (ADS)

Castro, Alonso; Shera, E. Brooks

1995-06-01

Recent developments in laser-based detection of fluorescent molecules have made possible the implementation of very sensitive techniques for biochemical analysis. We present and discuss our experiments on the applications of our recently developed technique of single-molecule detection to the analysis of molecules of biological interest. These newly developed methods are capable of detecting and identifying biomolecules at the single-molecule level of sensitivity. In one case, identification is based on measuring fluorescence brightness from single molecules. In another, molecules are classified by determining their electrophoretic velocities.

Preface: Special Topic on Single-Molecule Biophysics

NASA Astrophysics Data System (ADS)

Makarov, Dmitrii E.; Schuler, Benjamin

2018-03-01

Single-molecule measurements are now almost routinely used to study biological systems and processes. The scope of this special topic emphasizes the physics side of single-molecule observations, with the goal of highlighting new developments in physical techniques as well as conceptual insights that single-molecule measurements bring to biophysics. This issue also comprises recent advances in theoretical physical models of single-molecule phenomena, interpretation of single-molecule signals, and fundamental areas of statistical mechanics that are related to single-molecule observations. A particular goal is to illustrate the increasing synergy between theory, simulation, and experiment in single-molecule biophysics.

Combinatorial evolution of site- and enantioselective catalysts for polyene epoxidation

NASA Astrophysics Data System (ADS)

Lichtor, Phillip A.; Miller, Scott J.

2012-12-01

Selectivity in the catalytic functionalization of complex molecules is a major challenge in chemical synthesis. The problem is magnified when there are several possible stereochemical outcomes and when similar functional groups occur repeatedly within the same molecule. Selective polyene oxidation provides an archetypical example of this challenge. Historically, enzymatic catalysis has provided the only precedents. Although non-enzymatic catalysts that meet some of these challenges became known, a comprehensive solution has remained elusive. Here, we describe low molecular weight peptide-based catalysts, discovered through a combinatorial synthesis and screening protocol, that exhibit site- and enantioselective oxidation of certain positions of various isoprenols. This diversity-based approach, which exhibits features reminiscent of the directed evolution of enzymes, delivers catalysts that compare favourably to the state-of-the-art for the asymmetric oxidation of these compounds. Moreover, the approach culminated in catalysts that exhibit alternative-site selectivity in comparison to oxidation catalysts previously described.

Magnetic resonance microscopy: concepts, challenges, and state-of-the-art.

PubMed

Gimi, Barjor

2006-01-01

Recent strides in targeted therapy and regenerative medicine have created a need to identify molecules and metabolic pathways implicated in a disease and its treatment. These molecules and pathways must be discerned at the cellular level to meaningfully reveal the biochemical underpinnings of the disease and to identify key molecular targets for therapy. Magnetic resonance (MR) techniques are well suited for molecular and functional imaging because of their noninvasive nature and their versatility in extracting physiological, biochemical, and functional information over time. However, MR is an insensitive technique; MR microscopy seeks to increase detection sensitivity, thereby localizing biochemical and functional information at the level of single cells or small cellular clusters. Here, we discuss some of the challenges facing MR microscopy and the technical and phenomenological strategies used to overcome these challenges. Some of the applications of MR microscopy are highlighted in this chapter.

Toward the Space-Time Limit

NASA Astrophysics Data System (ADS)

Rios, Laura

A chemical reaction is fundamentally initiated by the restructuring of a chemical bond. Chemical reactions occur so quickly that their exact trajectory is unknown. To unlock the secret, first one would seek to know the inner working of a single molecule, and therein, a single chemical bond. However, the task is no small feat. Single molecule studies require exquisite spatial resolution afforded by relatively new technologies, and ultrafast laser techniques. The overarching theme of my dissertation will be the path towards achieving the space-time limit in chemistry: namely, the ability to record the structural changes of individual molecules during a reaction, one event at a time. A scanning tunneling microscope (STM) is used to image the molecules and manipulate their electronic environments. STM has the capacity to create topographical images of molecules with Angstrom ($10-10 m - the size of an atom) resolution, and can also probe the molecule electronically by use of a tunneling current (It). STM images reflect the changes in the potential energy surface (PES), and help us understand how molecules interact with surfaces and each other, thereby accessing the fundamental problem of catalysis and chemical reactions. In addition to seeing the molecule, we use Raman spectroscopy to track its molecular changes with chemical specificity. I combine these experimental tools to investigate tip-enhanced Raman spectra (TERS) of single molecules within the confines of a STM. These methods were used to report the conformational change of a single azobenzene-thiol derivative molecule. Although we were able to definitely isolate a single molecule signature, imaging the single molecule in real space and time proved elusive. Additionally, I report on a conductance switch based on the observable change of the topographic STM images of a radical anion mediated by the spin flip of a single electron on a single molecule. This is effectively the smallest achievable architecture of molecular electronics, negating the need for heat dissipation in small systems. A related work found how physisorption potentials of molecules to metals could be experimentally visually verified and modeled by STM, thus allowing us to use the STM tip as a driver for molecular motion on surfaces. Throughtout this work, we noted that a dominant feature of single molecule chemistry are intensity and spectral fluctuations that are difficult to characterize, as the molecule contorts wildly when it experiences distinct and powerful electromagnetic fields and field gradients. This much is evident in the last experiment, and chapter, of this thesis. Raman spectra associated with cobalt (II) tetraphenyl porphyrin (CoTPP) axially coordinated with bipyridyl ethylene (BPE) were captured with Raman mapping with nanometer resolution. However, the stochastic apperance of Raman lines and low resolution images made it difficult to ascertain which molecule we captured. The preliminary results as well as follow-up control experiments are discussed. While each experiment constitutes in and of itself an important, individual contribution, their sum establishes the principles of seeing single-molecule chemistry.

Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge.

PubMed

Bannan, Caitlin C; Burley, Kalistyn H; Chiu, Michael; Shirts, Michael R; Gilson, Michael K; Mobley, David L

2016-11-01

In the recent SAMPL5 challenge, participants submitted predictions for cyclohexane/water distribution coefficients for a set of 53 small molecules. Distribution coefficients (log D) replace the hydration free energies that were a central part of the past five SAMPL challenges. A wide variety of computational methods were represented by the 76 submissions from 18 participating groups. Here, we analyze submissions by a variety of error metrics and provide details for a number of reference calculations we performed. As in the SAMPL4 challenge, we assessed the ability of participants to evaluate not just their statistical uncertainty, but their model uncertainty-how well they can predict the magnitude of their model or force field error for specific predictions. Unfortunately, this remains an area where prediction and analysis need improvement. In SAMPL4 the top performing submissions achieved a root-mean-squared error (RMSE) around 1.5 kcal/mol. If we anticipate accuracy in log D predictions to be similar to the hydration free energy predictions in SAMPL4, the expected error here would be around 1.54 log units. Only a few submissions had an RMSE below 2.5 log units in their predicted log D values. However, distribution coefficients introduced complexities not present in past SAMPL challenges, including tautomer enumeration, that are likely to be important in predicting biomolecular properties of interest to drug discovery, therefore some decrease in accuracy would be expected. Overall, the SAMPL5 distribution coefficient challenge provided great insight into the importance of modeling a variety of physical effects. We believe these types of measurements will be a promising source of data for future blind challenges, especially in view of the relatively straightforward nature of the experiments and the level of insight provided.

Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge

PubMed Central

Bannan, Caitlin C.; Burley, Kalistyn H.; Chiu, Michael; Shirts, Michael R.; Gilson, Michael K.; Mobley, David L.

2016-01-01

In the recent SAMPL5 challenge, participants submitted predictions for cyclohexane/water distribution coefficients for a set of 53 small molecules. Distribution coefficients (log D) replace the hydration free energies that were a central part of the past five SAMPL challenges. A wide variety of computational methods were represented by the 76 submissions from 18 participating groups. Here, we analyze submissions by a variety of error metrics and provide details for a number of reference calculations we performed. As in the SAMPL4 challenge, we assessed the ability of participants to evaluate not just their statistical uncertainty, but their model uncertainty – how well they can predict the magnitude of their model or force field error for specific predictions. Unfortunately, this remains an area where prediction and analysis need improvement. In SAMPL4 the top performing submissions achieved a root-mean-squared error (RMSE) around 1.5 kcal/mol. If we anticipate accuracy in log D predictions to be similar to the hydration free energy predictions in SAMPL4, the expected error here would be around 1.54 log units. Only a few submissions had an RMSE below 2.5 log units in their predicted log D values. However, distribution coefficients introduced complexities not present in past SAMPL challenges, including tautomer enumeration, that are likely to be important in predicting biomolecular properties of interest to drug discovery, therefore some decrease in accuracy would be expected. Overall, the SAMPL5 distribution coefficient challenge provided great insight into the importance of modeling a variety of physical effects. We believe these types of measurements will be a promising source of data for future blind challenges, especially in view of the relatively straightforward nature of the experiments and the level of insight provided. PMID:27677750

Chiral selection on inorganic crystalline surfaces

NASA Technical Reports Server (NTRS)

Hazen, Robert M.; Sholl, David S.

2003-01-01

From synthetic drugs to biodegradable plastics to the origin of life, the chiral selection of molecules presents both daunting challenges and significant opportunities in materials science. Among the most promising, yet little explored, avenues for chiral molecular discrimination is adsorption on chiral crystalline surfaces - periodic environments that can select, concentrate and possibly even organize molecules into polymers and other macromolecular structures. Here we review experimental and theoretical approaches to chiral selection on inorganic crystalline surfaces - research that is poised to open this new frontier in understanding and exploiting surface-molecule interactions.

Multichannel microformulators for massively parallel machine learning and automated design of biological experiments

NASA Astrophysics Data System (ADS)

Wikswo, John; Kolli, Aditya; Shankaran, Harish; Wagoner, Matthew; Mettetal, Jerome; Reiserer, Ronald; Gerken, Gregory; Britt, Clayton; Schaffer, David

Genetic, proteomic, and metabolic networks describing biological signaling can have 102 to 103 nodes. Transcriptomics and mass spectrometry can quantify 104 different dynamical experimental variables recorded from in vitro experiments with a time resolution approaching 1 s. It is difficult to infer metabolic and signaling models from such massive data sets, and it is unlikely that causality can be determined simply from observed temporal correlations. There is a need to design and apply specific system perturbations, which will be difficult to perform manually with 10 to 102 externally controlled variables. Machine learning and optimal experimental design can select an experiment that best discriminates between multiple conflicting models, but a remaining problem is to control in real time multiple variables in the form of concentrations of growth factors, toxins, nutrients and other signaling molecules. With time-division multiplexing, a microfluidic MicroFormulator (μF) can create in real time complex mixtures of reagents in volumes suitable for biological experiments. Initial 96-channel μF implementations control the exposure profile of cells in a 96-well plate to different temporal profiles of drugs; future experiments will include challenge compounds. Funded in part by AstraZeneca, NIH/NCATS HHSN271201600009C and UH3TR000491, and VIIBRE.

Global molecular identification from graphs. Neutral and ionized main-group diatomic molecules.

PubMed

James, Bryan; Caviness, Ken; Geach, Jonathan; Walters, Chris; Hefferlin, Ray

2002-01-01

Diophantine equations and inequalities are presented for main-group closed-shell diatomic molecules. Specifying various bond types (covalent, dative, ionic, van der Waals) and multiplicities, it becomes possible to identify all possible molecules. While many of the identified species are probably unstable under normal conditions, they are interesting and present a challenge for computational or experimental analysis. Ionized molecules with net charges of -1, 1, and 2 are also identified. The analysis applies to molecules with atoms from periods 2 and 3 but can be generalized by substituting isovalent atoms. When closed-shell neutral diatomics are positioned in the chemical space (with axes enumerating the numbers of valence electrons of the free atoms), it is seen that they lie on a few parallel isoelectronic series.

Histone-poly(A) hybrid molecules as tools to block nuclear pores.

PubMed

Cremer, G; Wojtech, E; Kalbas, M; Agutter, P S; Prochnow, D

1995-04-01

Histone-poly(A) hybrid molecules were used for transport experiments with resealed nuclear envelopes and after attachment of a cleavable cross-linker (SASD) to identify nuclear proteins. In contrast to histones, the hybrid molecules cannot be accumulated in resealed nuclear envelopes, and in contrast to poly(A), the export of hybrids from preloaded nuclear envelopes is completely impaired. The experiments strongly confirm the existence of poly(A) as an export signal in mRNA which counteracts the nuclear location signals (NLS) in histones. The contradicting transport signals in the hybrid molecules impair translocation through the nuclear pore complex. The failure to accumulate hybrid molecules into resealed nuclear envelopes results from the covalent attachment of polyadenylic acid to histones in a strict 1:1 molar ratio. This was demonstrated in control transport experiments where radiolabeled histones were simply mixed with nonlabeled poly(A) or radiolabeled poly(A) mixed with nonlabeled histones. In comparison, control uptake experiments with histones covalently linked to a single UMP-mononucleotide are strongly enhanced. Such controls exclude the conceivable possibility of a simple masking of the nuclear location signal in the histones by the covalent attached poly(A) moiety. Photoreactive histone-poly(A) hybrid analogs serve to identify nuclear envelope proteins--presumably in the nuclear pore--with molecular weights of 110, 80, and 71.4 kDa.

Towards a molecular logic machine

NASA Astrophysics Data System (ADS)

Remacle, F.; Levine, R. D.

2001-06-01

Finite state logic machines can be realized by pump-probe spectroscopic experiments on an isolated molecule. The most elaborate setup, a Turing machine, can be programmed to carry out a specific computation. We argue that a molecule can be similarly programmed, and provide examples using two photon spectroscopies. The states of the molecule serve as the possible states of the head of the Turing machine and the physics of the problem determines the possible instructions of the program. The tape is written in an alphabet that allows the listing of the different pump and probe signals that are applied in a given experiment. Different experiments using the same set of molecular levels correspond to different tapes that can be read and processed by the same head and program. The analogy to a Turing machine is not a mechanical one and is not completely molecular because the tape is not part of the molecular machine. We therefore also discuss molecular finite state machines, such as sequential devices, for which the tape is not part of the machine. Nonmolecular tapes allow for quite long input sequences with a rich alphabet (at the level of 7 bits) and laser pulse shaping experiments provide concrete examples. Single molecule spectroscopies show that a single molecule can be repeatedly cycled through a logical operation.

Computational biology of RNA interactions.

PubMed

Dieterich, Christoph; Stadler, Peter F

2013-01-01

The biodiversity of the RNA world has been underestimated for decades. RNA molecules are key building blocks, sensors, and regulators of modern cells. The biological function of RNA molecules cannot be separated from their ability to bind to and interact with a wide space of chemical species, including small molecules, nucleic acids, and proteins. Computational chemists, physicists, and biologists have developed a rich tool set for modeling and predicting RNA interactions. These interactions are to some extent determined by the binding conformation of the RNA molecule. RNA binding conformations are approximated with often acceptable accuracy by sequence and secondary structure motifs. Secondary structure ensembles of a given RNA molecule can be efficiently computed in many relevant situations by employing a standard energy model for base pair interactions and dynamic programming techniques. The case of bi-molecular RNA-RNA interactions can be seen as an extension of this approach. However, unbiased transcriptome-wide scans for local RNA-RNA interactions are computationally challenging yet become efficient if the binding motif/mode is known and other external information can be used to confine the search space. Computational methods are less developed for proteins and small molecules, which bind to RNA with very high specificity. Binding descriptors of proteins are usually determined by in vitro high-throughput assays (e.g., microarrays or sequencing). Intriguingly, recent experimental advances, which are mostly based on light-induced cross-linking of binding partners, render in vivo binding patterns accessible yet require new computational methods for careful data interpretation. The grand challenge is to model the in vivo situation where a complex interplay of RNA binders competes for the same target RNA molecule. Evidently, bioinformaticians are just catching up with the impressive pace of these developments. Copyright © 2012 John Wiley & Sons, Ltd.

Insight into the molecular mechanism of water evaporation via the finite temperature string method.

PubMed

Musolino, Nicholas; Trout, Bernhardt L

2013-04-07

The process of water's evaporation at its liquid/air interface has proven challenging to study experimentally and, because it constitutes a rare event on molecular time scales, presents a challenge for computer simulations as well. In this work, we simulated water's evaporation using the classical extended simple point charge model water model, and identified a minimum free energy path for this process in terms of 10 descriptive order parameters. The measured free energy change was 7.4 kcal/mol at 298 K, in reasonable agreement with the experimental value of 6.3 kcal/mol, and the mean first-passage time was 1375 ns for a single molecule, corresponding to an evaporation coefficient of 0.25. In the observed minimum free energy process, the water molecule diffuses to the surface, and tends to rotate so that its dipole and one O-H bond are oriented outward as it crosses the Gibbs dividing surface. As the water molecule moves further outward through the interfacial region, its local density is higher than the time-averaged density, indicating a local solvation shell that protrudes from the interface. The water molecule loses donor and acceptor hydrogen bonds, and then, with its dipole nearly normal to the interface, stops donating its remaining hydrogen bond. At that point, when the final, accepted hydrogen bond is broken, the water molecule is free. We also analyzed which order parameters are most important in the process and in reactive trajectories, and found that the relative orientation of water molecules near the evaporating molecule, and the number of accepted hydrogen bonds, were important variables in reactive trajectories and in kinetic descriptions of the process.

Deciphering the Landauer-Büttiker Transmission Function from Single Molecule Break Junction Experiments

NASA Astrophysics Data System (ADS)

Reuter, Matthew; Tschudi, Stephen

When investigating the electrical response properties of molecules, experiments often measure conductance whereas computation predicts transmission probabilities. Although the Landauer-Büttiker theory relates the two in the limit of coherent scattering through the molecule, a direct comparison between experiment and computation can still be difficult. Experimental data (specifically that from break junctions) is statistical and computational results are deterministic. Many studies compare the most probable experimental conductance with computation, but such an analysis discards almost all of the experimental statistics. In this work we develop tools to decipher the Landauer-Büttiker transmission function directly from experimental statistics and then apply them to enable a fairer comparison between experimental and computational results.

Protein based therapeutic delivery agents: Contemporary developments and challenges.

PubMed

Yin, Liming; Yuvienco, Carlo; Montclare, Jin Kim

2017-07-01

As unique biopolymers, proteins can be employed for therapeutic delivery. They bear important features such as bioavailability, biocompatibility, and biodegradability with low toxicity serving as a platform for delivery of various small molecule therapeutics, gene therapies, protein biologics and cells. Depending on size and characteristic of the therapeutic, a variety of natural and engineered proteins or peptides have been developed. This, coupled to recent advances in synthetic and chemical biology, has led to the creation of tailor-made protein materials for delivery. This review highlights strategies employing proteins to facilitate the delivery of therapeutic matter, addressing the challenges for small molecule, gene, protein and cell transport. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular insights into the stabilization of protein-protein interactions with small molecule: The FKBP12-rapamycin-FRB case study

NASA Astrophysics Data System (ADS)

Chaurasia, Shilpi; Pieraccini, Stefano; De Gonda, Riccardo; Conti, Simone; Sironi, Maurizio

2013-11-01

Targetting protein-protein interactions is a challenging task in drug discovery process. Despite the challenges, several studies provided evidences for the development of small molecules modulating protein-protein interactions. Here we consider a typical case of protein-protein interaction stabilization: the complex between FKBP12 and FRB with rapamycin. We have analyzed the stability of the complex and characterized its interactions at the atomic level by performing free energy calculations and computational alanine scanning. It is shown that rapamycin stabilizes the complex by acting as a bridge between the two proteins; and the complex is stable only in the presence of rapamycin.

Bioastrophysical aspects of low energy ion irradiation of frozen anthracene containing water.

PubMed

Tuleta, M; Gabła, L; Madej, J

2001-08-13

The origin of life on Earth remains a fascinating mystery in spite of many theories existing on this subject. However, it seems that simple prebiotic molecules could play an essential role in the formation of more complex organisms. In our experiment, we synthesized a class of these molecules (quinones) bombarding frozen anthracene containing water with low energy hydrogen ions. This experiment roughly simulated the astrophysical conditions which one can find in the solar system. Thus, we can hypothesize that prebiotic molecules could be created by interaction of the solar wind with interplanetary dust grains. The delivery of these molecules to early Earth may have contributed to the generation of life on our planet.

Accessing non-natural reactivity by irradiating nicotinamide-dependent enzymes with light

NASA Astrophysics Data System (ADS)

Emmanuel, Megan A.; Greenberg, Norman R.; Oblinsky, Daniel G.; Hyster, Todd K.

2016-12-01

Enzymes are ideal for use in asymmetric catalysis by the chemical industry, because their chemical compositions can be tailored to a specific substrate and selectivity pattern while providing efficiencies and selectivities that surpass those of classical synthetic methods. However, enzymes are limited to reactions that are found in nature and, as such, facilitate fewer types of transformation than do other forms of catalysis. Thus, a longstanding challenge in the field of biologically mediated catalysis has been to develop enzymes with new catalytic functions. Here we describe a method for achieving catalytic promiscuity that uses the photoexcited state of nicotinamide co-factors (molecules that assist enzyme-mediated catalysis). Under irradiation with visible light, the nicotinamide-dependent enzyme known as ketoreductase can be transformed from a carbonyl reductase into an initiator of radical species and a chiral source of hydrogen atoms. We demonstrate this new reactivity through a highly enantioselective radical dehalogenation of lactones—a challenging transformation for small-molecule catalysts. Mechanistic experiments support the theory that a radical species acts as an intermediate in this reaction, with NADH and NADPH (the reduced forms of nicotinamide adenine nucleotide and nicotinamide adenine dinucleotide phosphate, respectively) serving as both a photoreductant and the source of hydrogen atoms. To our knowledge, this method represents the first example of photo-induced enzyme promiscuity, and highlights the potential for accessing new reactivity from existing enzymes simply by using the excited states of common biological co-factors. This represents a departure from existing light-driven biocatalytic techniques, which are typically explored in the context of co-factor regeneration.

DNA-Based Single-Molecule Electronics: From Concept to Function.

PubMed

Wang, Kun

2018-01-17

Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics. This review gives a brief survey of recent experimental progress in DNA-based single-molecule electronics with special focus on single-molecule conductance and I-V characteristics of individual DNA molecules. Existing challenges and exciting future opportunities are also discussed.

DNA-Based Single-Molecule Electronics: From Concept to Function

PubMed Central

2018-01-01

Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics. This review gives a brief survey of recent experimental progress in DNA-based single-molecule electronics with special focus on single-molecule conductance and I–V characteristics of individual DNA molecules. Existing challenges and exciting future opportunities are also discussed. PMID:29342091

Mapping the energy landscape for second-stage folding of a single membrane protein

PubMed Central

Min, Duyoung; Jefferson, Robert E; Bowie, James U; Yoon, Tae-Young

2016-01-01

Membrane proteins are designed to fold and function in a lipid membrane, yet folding experiments within a native membrane environment are challenging to design. Here we show that single-molecule forced unfolding experiments can be adapted to study helical membrane protein folding under native-like bicelle conditions. Applying force using magnetic tweezers, we find that a transmembrane helix protein, Escherichia coli rhomboid protease GlpG, unfolds in a highly cooperative manner, largely unraveling as one physical unit in response to mechanical tension above 25 pN. Considerable hysteresis is observed, with refolding occurring only at forces below 5 pN. Characterizing the energy landscape reveals only modest thermodynamic stability (ΔG = 6.5 kBT) but a large unfolding barrier (21.3 kBT) that can maintain the protein in a folded state for long periods of time (t1/2 ~3.5 h). The observed energy landscape may have evolved to limit the existence of troublesome partially unfolded states and impart rigidity to the structure. PMID:26479439

Bringing research into a first semester organic chemistry laboratory with the multistep synthesis of carbohydrate-based HIV inhibitor mimics.

PubMed

Pontrello, Jason K

2015-01-01

Benefits of incorporating research experiences into laboratory courses have been well documented, yet examples of research projects designed for the first semester introductory organic chemistry lab course are extremely rare. To address this deficiency, a Carbohydrate-Based human immunodeficiency virus (HIV) Inhibitor project consisting of a synthetic scheme of four reactions was developed for and implemented in the first semester organic lab. Students carried out the synthetic reactions during the last 6 of 10 total labs in the course, generating carbohydrate-based dimeric target molecules modeled after published dimers with application in HIV therapy. The project was designed to provide a research experience through use of literature procedures for reactions performed, exploration of variation in linker length in the target structure, and synthesis of compounds not previously reported in the scientific literature. Project assessment revealed strong student support, indicating enhanced engagement and interest in the course as a direct result of the use of scientific literature and the applications of the synthesized carbohydrate-based molecules. Regardless of discussed challenges in designing a research project for the first semester lab course, the finding from data analysis that a project implemented in the first semester lab had significantly greater student impact than a second semester project should provide motivation for development of additional research projects for a first semester organic course. © 2015 The International Union of Biochemistry and Molecular Biology.

A reaction-diffusion model of cytosolic hydrogen peroxide.

PubMed

Lim, Joseph B; Langford, Troy F; Huang, Beijing K; Deen, William M; Sikes, Hadley D

2016-01-01

As a signaling molecule in mammalian cells, hydrogen peroxide (H2O2) determines the thiol/disulfide oxidation state of several key proteins in the cytosol. Localization is a key concept in redox signaling; the concentrations of signaling molecules within the cell are expected to vary in time and in space in manner that is essential for function. However, as a simplification, all theoretical studies of intracellular hydrogen peroxide and many experimental studies to date have treated the cytosol as a well-mixed compartment. In this work, we incorporate our previously reported reduced kinetic model of the network of reactions that metabolize hydrogen peroxide in the cytosol into a model that explicitly treats diffusion along with reaction. We modeled a bolus addition experiment, solved the model analytically, and used the resulting equations to quantify the spatiotemporal variations in intracellular H2O2 that result from this kind of perturbation to the extracellular H2O2 concentration. We predict that micromolar bolus additions of H2O2 to suspensions of HeLa cells (0.8 × 10(9)cells/l) result in increases in the intracellular concentration that are localized near the membrane. These findings challenge the assumption that intracellular concentrations of H2O2 are increased uniformly throughout the cell during bolus addition experiments and provide a theoretical basis for differing phenotypic responses of cells to intracellular versus extracellular perturbations to H2O2 levels. Copyright © 2015 Elsevier Inc. All rights reserved.

Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation.

PubMed

Hiatt, Joseph B; Pritchard, Colin C; Salipante, Stephen J; O'Roak, Brian J; Shendure, Jay

2013-05-01

The detection and quantification of genetic heterogeneity in populations of cells is fundamentally important to diverse fields, ranging from microbial evolution to human cancer genetics. However, despite the cost and throughput advances associated with massively parallel sequencing, it remains challenging to reliably detect mutations that are present at a low relative abundance in a given DNA sample. Here we describe smMIP, an assay that combines single molecule tagging with multiplex targeted capture to enable practical and highly sensitive detection of low-frequency or subclonal variation. To demonstrate the potential of the method, we simultaneously resequenced 33 clinically informative cancer genes in eight cell line and 45 clinical cancer samples. Single molecule tagging facilitated extremely accurate consensus calling, with an estimated per-base error rate of 8.4 × 10(-6) in cell lines and 2.6 × 10(-5) in clinical specimens. False-positive mutations in the single molecule consensus base-calls exhibited patterns predominantly consistent with DNA damage, including 8-oxo-guanine and spontaneous deamination of cytosine. Based on mixing experiments with cell line samples, sensitivity for mutations above 1% frequency was 83% with no false positives. At clinically informative sites, we identified seven low-frequency point mutations (0.2%-4.7%), including BRAF p.V600E (melanoma, 0.2% alternate allele frequency), KRAS p.G12V (lung, 0.6%), JAK2 p.V617F (melanoma, colon, two lung, 0.3%-1.4%), and NRAS p.Q61R (colon, 4.7%). We anticipate that smMIP will be broadly adoptable as a practical and effective method for accurately detecting low-frequency mutations in both research and clinical settings.

Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation

PubMed Central

Hiatt, Joseph B.; Pritchard, Colin C.; Salipante, Stephen J.; O'Roak, Brian J.; Shendure, Jay

2013-01-01

The detection and quantification of genetic heterogeneity in populations of cells is fundamentally important to diverse fields, ranging from microbial evolution to human cancer genetics. However, despite the cost and throughput advances associated with massively parallel sequencing, it remains challenging to reliably detect mutations that are present at a low relative abundance in a given DNA sample. Here we describe smMIP, an assay that combines single molecule tagging with multiplex targeted capture to enable practical and highly sensitive detection of low-frequency or subclonal variation. To demonstrate the potential of the method, we simultaneously resequenced 33 clinically informative cancer genes in eight cell line and 45 clinical cancer samples. Single molecule tagging facilitated extremely accurate consensus calling, with an estimated per-base error rate of 8.4 × 10−6 in cell lines and 2.6 × 10−5 in clinical specimens. False-positive mutations in the single molecule consensus base-calls exhibited patterns predominantly consistent with DNA damage, including 8-oxo-guanine and spontaneous deamination of cytosine. Based on mixing experiments with cell line samples, sensitivity for mutations above 1% frequency was 83% with no false positives. At clinically informative sites, we identified seven low-frequency point mutations (0.2%–4.7%), including BRAF p.V600E (melanoma, 0.2% alternate allele frequency), KRAS p.G12V (lung, 0.6%), JAK2 p.V617F (melanoma, colon, two lung, 0.3%–1.4%), and NRAS p.Q61R (colon, 4.7%). We anticipate that smMIP will be broadly adoptable as a practical and effective method for accurately detecting low-frequency mutations in both research and clinical settings. PMID:23382536

Glass Transition and Molecular Mobility in Styrene-Butadiene Rubber Modified Asphalt.

PubMed

Khabaz, Fardin; Khare, Rajesh

2015-11-05

Asphalt, a soft matter consisting of more than a thousand chemical species, is of vital importance for the transportation infrastructure, yet it poses significant challenges for microscopic theory and modeling approaches due to its multicomponent nature. Polymeric additives can potentially enhance the thermo-mechanical properties of asphalt, thus helping reduce the road repair costs; rational design of such systems requires knowledge of the molecular structure and dynamics of these systems. We have used molecular dynamics (MD) simulations to investigate the volumetric, structural, and dynamic properties of the neat asphalt as well as styrene-butadiene rubber (SBR) modified asphalt systems. The volume-temperature behavior of the asphalt systems exhibited a glass transition phenomenon, akin to that observed in experiments. The glass transition temperature, room temperature density, and coefficient of volume thermal expansion of the neat asphalt systems so evaluated were in agreement with experimental data when the effect of the high cooling rate used in simulations was accounted for. While the volumetric properties of SBR modified asphalt were found to be insensitive to the presence of the SBR additive, the addition of SBR led to an increase in the aggregation of asphaltene molecules. Furthermore, addition of SBR caused a reduction in the mobility of the constituent molecules of asphalt, with the reduction being more significant for the larger constituent molecules. Similar to other glass forming liquids, the reciprocal of the diffusion coefficient of the selected molecules was observed to follow the Vogel-Fulcher-Tammann (VFT) behavior as a function of temperature. These results suggest the potential for using polymeric additives for enhancing the dynamic mechanical properties of asphalt without affecting its volumetric properties.

CAN ULTRASOUND ENABLE EFFICIENT INTRACELLULAR UPTAKE OF MOLECULES? A RETROSPECTIVE LITERATURE REVIEW AND ANALYSIS

PubMed Central

LIU, YING; YAN, JING; PRAUSNITZ, MARK R.

2012-01-01

Most applications of therapeutic ultrasound (US) for intracellular delivery of drugs, proteins, DNA/ RNA and other compounds would benefit from efficient uptake of these molecules into large numbers of cells without killing cells in the process. In this study we tested the hypothesis that efficient intracellular uptake of molecules can be achieved with high cell viability after US exposure in vitro. A search of the literature for studies with quantitative data on uptake and viability yielded 26 published papers containing 898 experimental data points. Analysis of these studies showed that just 7.7% of the data points corresponded to relatively efficient uptake (>50% of cells exhibiting uptake). Closer examination of the data showed that use of Definity US contrast agent (as opposed to Optison) and elevated sonication temperature at 37°C (as opposed to room temperature) were associated with high uptake, which we further validated through independent experiments carried out in this study. Although these factors contributed to high uptake, almost all data with efficient uptake were from studies that had not accounted for lysed cells when determining cell viability. Based on retrospective analysis of the data, we showed that not accounting for lysed cells can dramatically increase the calculated uptake efficiency. We further argue that if all the data considered in this study were re-analyzed to account for lysed cells, there would be essentially no data with efficient uptake. We therefore conclude that the literature does not support the hypothesis that efficient intracellular uptake of molecules can be achieved with high cell viability after US exposure in vitro, which poses a challenge to future applications of US that require efficient intracellular delivery. PMID:22425381

Anharmonic, dynamic and functional level effects in far-infrared spectroscopy: Phenol derivatives

NASA Astrophysics Data System (ADS)

Bakker, Daniël J.; Ong, Qin; Dey, Arghya; Mahé, Jérôme; Gaigeot, Marie-Pierre; Rijs, Anouk M.

2017-12-01

The far-infrared (far-IR) spectra of phenol and four ortho-substituted phenol derivatives, including three deuterated analogs, are presented. These spectra, measured using the free electron laser FELIX, are used to compare the performance of Born-Oppenheimer Molecular Dynamics (BOMD) with several commonly used levels of static density functional theory in the far-IR region. The molecules studied here form intramolecular hydrogen bonds of different strengths (except phenol), display diverse degrees of flexibility, and the OH moieties of the molecules provide large amplitude, anharmonic OH torsional modes. Since several of the molecules contain two OH groups, strong anharmonic couplings can also be present. Moreover, the experimental far-IR spectra of phenol and saligenin show overtones and combination bands as proven by the measurements of their deuterated analogs. All these characteristics of the molecules enable us to test the performance of the applied levels of theory on different complicating factors. Briefly summarized, both the strength of the hydrogen bond and molecular rigidity do not significantly influence the agreement between theory and experiment. All applied theoretical methods have difficulties to consistently predict modes that include the anharmonic OH torsional motion, resulting in overestimated intensities and frequencies. Coupling between two OH functional groups provides an additional challenge for theories, as seen for catechol. The various employed theoretical methods are found to complement each other, showing good results for complex harmonic modes in the case of static B3LYP-D3, while improved results are observed for anharmonic modes, including the OH torsional modes and their couplings, in the case of BOMD. Additionally, BOMD calculates the relative intensities better than the other theories. VPT2 reproduces weak anharmonic modes well, but it overestimates shifts and intensities for strong anharmonic modes.

Tracking the ultrafast motion of a single molecule by femtosecond orbital imaging

NASA Astrophysics Data System (ADS)

Cocker, Tyler L.; Peller, Dominik; Yu, Ping; Repp, Jascha; Huber, Rupert

2016-11-01

Watching a single molecule move on its intrinsic timescale has been one of the central goals of modern nanoscience, and calls for measurements that combine ultrafast temporal resolution with atomic spatial resolution. Steady-state experiments access the requisite spatial scales, as illustrated by direct imaging of individual molecular orbitals using scanning tunnelling microscopy or the acquisition of tip-enhanced Raman and luminescence spectra with sub-molecular resolution. But tracking the intrinsic dynamics of a single molecule directly in the time domain faces the challenge that interactions with the molecule must be confined to a femtosecond time window. For individual nanoparticles, such ultrafast temporal confinement has been demonstrated by combining scanning tunnelling microscopy with so-called lightwave electronics, which uses the oscillating carrier wave of tailored light pulses to directly manipulate electronic motion on timescales faster even than a single cycle of light. Here we build on ultrafast terahertz scanning tunnelling microscopy to access a state-selective tunnelling regime, where the peak of a terahertz electric-field waveform transiently opens an otherwise forbidden tunnelling channel through a single molecular state. It thereby removes a single electron from an individual pentacene molecule’s highest occupied molecular orbital within a time window shorter than one oscillation cycle of the terahertz wave. We exploit this effect to record approximately 100-femtosecond snapshot images of the orbital structure with sub-ångström spatial resolution, and to reveal, through pump/probe measurements, coherent molecular vibrations at terahertz frequencies directly in the time domain. We anticipate that the combination of lightwave electronics and the atomic resolution of our approach will open the door to visualizing ultrafast photochemistry and the operation of molecular electronics on the single-orbital scale.

Quantum Chemical Studies of Actinides and Lanthanides: From Small Molecules to Nanoclusters

NASA Astrophysics Data System (ADS)

Vlaisavljevich, Bess

Research into actinides is of high interest because of their potential applications as an energy source and for the environmental implications therein. Global concern has arisen since the development of the actinide concept in the 1940s led to the industrial scale use of the commercial nuclear energy cycle and nuclear weapons production. Large quantities of waste have been generated from these processes inspiring efforts to address fundamental questions in actinide science. In this regard, the objective of this work is to use theory to provide insight and predictions into actinide chemistry, where experimental work is extremely challenging because of the intrinsic difficulties of the experiments themselves and the safety issues associated with this type of chemistry. This thesis is a collection of theoretical studies of actinide chemistry falling into three categories: quantum chemical and matrix isolation studies of small molecules, the electronic structure of organoactinide systems, and uranyl peroxide nanoclusters and other solid state actinide compounds. The work herein not only spans a wide range of systems size but also investigates a range of chemical problems. Various quantum chemical approaches have been employed. Wave function-based methods have been used to study the electronic structure of actinide containing molecules of small to middle-size. Among these methods, the complete active space self consistent field (CASSCF) approach with corrections from second-order perturbation theory (CASPT2), the generalized active space SCF (GASSCF) approach, and Moller-Plesset second-order perturbation theory (MP2) have been employed. Likewise, density functional theory (DFT) has been used along with analysis tools like bond energy decomposition, bond orders, and Bader's Atoms in Molecules. From these quantum chemical results, comparison with experimentally obtained structures and spectra are made.

Biology and polymer physics at the single-molecule level.

PubMed

Chu, Steven

2003-04-15

The ability to look at individual molecules has given us new insights into molecular processes. Examples of our recent work are given to illustrate how behaviour that may otherwise be hidden from view can be clearly seen in single-molecule experiments.

SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy

PubMed Central

Tang, Yunqing; Dai, Luru; Zhang, Xiaoming; Li, Junbai; Hendriks, Johnny; Fan, Xiaoming; Gruteser, Nadine; Meisenberg, Annika; Baumann, Arnd; Katranidis, Alexandros; Gensch, Thomas

2015-01-01

Single molecule localization based super-resolution fluorescence microscopy offers significantly higher spatial resolution than predicted by Abbe’s resolution limit for far field optical microscopy. Such super-resolution images are reconstructed from wide-field or total internal reflection single molecule fluorescence recordings. Discrimination between emission of single fluorescent molecules and background noise fluctuations remains a great challenge in current data analysis. Here we present a real-time, and robust single molecule identification and localization algorithm, SNSMIL (Shot Noise based Single Molecule Identification and Localization). This algorithm is based on the intrinsic nature of noise, i.e., its Poisson or shot noise characteristics and a new identification criterion, QSNSMIL, is defined. SNSMIL improves the identification accuracy of single fluorescent molecules in experimental or simulated datasets with high and inhomogeneous background. The implementation of SNSMIL relies on a graphics processing unit (GPU), making real-time analysis feasible as shown for real experimental and simulated datasets. PMID:26098742

Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations

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

Fischer, Sean A.; Aprà, Edoardo; Govind, Niranjan

2017-02-03

Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single molecule SERS spectra and selection rules is a challenging task, and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4’-dimercaptostilbene, DMS) interacting withmore » a metallic cluster (Ag20). This affects our simulated single molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.« less

Stem cells as delivery vehicles for regenerative medicine-challenges and perspectives

PubMed Central

Labusca, Luminita; Herea, Dumitru Daniel; Mashayekhi, Kaveh

2018-01-01

The use of stem cells as carriers for therapeutic agents is an appealing modality for targeting tissues or organs of interest. Combined delivery of cells together with various information molecules as therapeutic agents has the potential to enhance, modulate or even initiate local or systemic repair processes, increasing stem cell efficiency for regenerative medicine applications. Stem-cell-mediated delivery of genes, proteins or small molecules takes advantage of the innate capability of stem cells to migrate and home to injury sites. As the native migratory properties are affected by in vitro expansion, the existent methods for enhancing stem cell targeting capabilities (modified culture methods, genetic modification, cell surface engineering) are described. The role of various nanoparticles in equipping stem cells with therapeutic small molecules is revised together with their class-specific advantages and shortcomings. Modalities to circumvent common challenges when designing a stem-cell-mediated targeted delivery system are described as well as future prospects in using this approach for regenerative medicine applications. PMID:29849930

Discovery of functional monoclonal antibodies targeting G-protein-coupled receptors and ion channels.

PubMed

Wilkinson, Trevor C I

2016-06-15

The development of recombinant antibody therapeutics is a significant area of growth in the pharmaceutical industry with almost 50 approved monoclonal antibodies on the market in the US and Europe. Despite this growth, however, certain classes of important molecular targets have remained intractable to therapeutic antibodies due to complexity of the target molecules. These complex target molecules include G-protein-coupled receptors and ion channels which represent a large potential target class for therapeutic intervention with monoclonal antibodies. Although these targets have typically been addressed by small molecule approaches, the exquisite specificity of antibodies provides a significant opportunity to provide selective modulation of these target proteins. Given this opportunity, substantial effort has been applied to address the technical challenges of targeting these complex membrane proteins with monoclonal antibodies. In this review recent progress made in the strategies for discovery of functional monoclonal antibodies for these challenging membrane protein targets is addressed. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

Directed assembly of nanomaterials for miniaturized sensors by dip-pen nanolithography using precursor inks

NASA Astrophysics Data System (ADS)

Su, Ming

The advent of nanomaterials with enhanced properties and the means to pattern them in a controlled fashion have paved the way to construct miniaturized sensors for improved detection. However it remains a challenge for the traditional methods to create such sensors and sensor arrays. Dip pen nanolithography (DPN) can form nanostructures on a substrate by controlling the transfer of molecule inks. However, previous DPN can not pattern solid materials on insulating surfaces, which are necessary to form functional electronic devices. In the dissertation, the concept of reactive precursor inks for DPN is developed for the generation of solid functional nanostructures of the following materials: organic molecule, sol-gel material, and conducting polymer. First, the covalent bonding is unnecessary for DPN as shown in the colored ink DPN; therefore the numbers of molecules that can be patterned is extended beyond thiol or thiolated molecules. Subsequently, a reactive precursor strategy (sol) is developed to pattern inorganic or organic/inorganic composite nanostructures on silicon based substrates. The method works by hydrolysis of metal precursors in the water meniscus and allows the preparation of solid structures with controlled geometry beyond the individual molecule level. Then the SnO 2 nanostructures patterned between the gaps of electrodes are tested as gas sensors. Proof-of-concept experiments are demonstrated on miniaturized sensors that show fast response and recovery to certain gases. Furthermore, an eight-unit sensor array is fabricated on a chip using SnO2 sols that are doped with different metals. The multiplexed device can recognize different gases by comparing the response patterns with the reference patterns of known gases generated on the same array. At last, the idea of precursor ink for DPN is extended to construct conducting polymer based devices. By using an acid promoted polymerization approach, conducting polymers are patterned on silicon dioxide substrates. The patterned organic solids response to light and behave as miniaturized photo-detectors. The microstructures are studied using microscopic and spectroscopic techniques.

Resolving Fast, Confined Diffusion in Bacteria with Image Correlation Spectroscopy.

PubMed

Rowland, David J; Tuson, Hannah H; Biteen, Julie S

2016-05-24

By following single fluorescent molecules in a microscope, single-particle tracking (SPT) can measure diffusion and binding on the nanometer and millisecond scales. Still, although SPT can at its limits characterize the fastest biomolecules as they interact with subcellular environments, this measurement may require advanced illumination techniques such as stroboscopic illumination. Here, we address the challenge of measuring fast subcellular motion by instead analyzing single-molecule data with spatiotemporal image correlation spectroscopy (STICS) with a focus on measurements of confined motion. Our SPT and STICS analysis of simulations of the fast diffusion of confined molecules shows that image blur affects both STICS and SPT, and we find biased diffusion rate measurements for STICS analysis in the limits of fast diffusion and tight confinement due to fitting STICS correlation functions to a Gaussian approximation. However, we determine that with STICS, it is possible to correctly interpret the motion that blurs single-molecule images without advanced illumination techniques or fast cameras. In particular, we present a method to overcome the bias due to image blur by properly estimating the width of the correlation function by directly calculating the correlation function variance instead of using the typical Gaussian fitting procedure. Our simulation results are validated by applying the STICS method to experimental measurements of fast, confined motion: we measure the diffusion of cytosolic mMaple3 in living Escherichia coli cells at 25 frames/s under continuous illumination to illustrate the utility of STICS in an experimental parameter regime for which in-frame motion prevents SPT and tight confinement of fast diffusion precludes stroboscopic illumination. Overall, our application of STICS to freely diffusing cytosolic protein in small cells extends the utility of single-molecule experiments to the regime of fast confined diffusion without requiring advanced microscopy techniques. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Insight into hydrogen bonds and characterization of interlayer spacing of hydrated graphene oxide.

PubMed

Liu, Liyan; Zhang, Ruifeng; Liu, Ying; Tan, Wei; Zhu, Guorui

2018-05-28

The number of hydrogen bonds and detailed information on the interlayer spacing of graphene oxide (GO) confined water molecules were calculated through experiments and molecular dynamics simulations. Experiments play a crucial role in the modeling strategy and verification of the simulation results. The binding of GO and water molecules is essentially controlled by hydrogen bond networks involving functional groups and water molecules confined in the GO layers. With the increase in the water content, the clusters of water molecules are more evident. The water molecules bounding to GO layers are transformed to a free state, making the removal of water molecules from the system difficult at low water contents. The diffuse behaviors of the water molecules are more evident at high water contents. With an increase in the water content, the functional groups are surrounded by fewer water molecules, and the distance between the functional groups and water molecules increases. As a result, the water molecules adsorbed into the GO interlamination will enlarge the interlayer spacing. The interlayer spacing is also affected by the number of GO layers. These results were confirmed by the calculations of number of hydrogen bonds, water state, mean square displacement, radial distribution function, and interlayer spacing of hydrated GO. Graphical Abstract This work research the interaction between GO functional groups and confined water molecules. The state of water molecules and interlayer spacing of graphene oxide were proved to be related to the number of hydrogen bonds.

Development of therapeutic antibodies to G protein-coupled receptors and ion channels: Opportunities, challenges and their therapeutic potential in respiratory diseases.

PubMed

Douthwaite, Julie A; Finch, Donna K; Mustelin, Tomas; Wilkinson, Trevor C I

2017-01-01

The development of recombinant antibody therapeutics continues to be a significant area of growth in the pharmaceutical industry with almost 50 approved monoclonal antibodies on the market in the US and Europe. Therapeutic drug targets such as soluble cytokines, growth factors and single transmembrane spanning receptors have been successfully targeted by recombinant monoclonal antibodies and the development of new product candidates continues. Despite this growth, however, certain classes of important disease targets have remained intractable to therapeutic antibodies due to the complexity of the target molecules. These complex target molecules include G protein-coupled receptors and ion channels which represent a large target class for therapeutic intervention with monoclonal antibodies. Although these targets have typically been addressed by small molecule approaches, the exquisite specificity of antibodies provides a significant opportunity to provide selective modulation of these important regulators of cell function. Given this opportunity, a significant effort has been applied to address the challenges of targeting these complex molecules and a number of targets are linked to the pathophysiology of respiratory diseases. In this review, we provide a summary of the importance of GPCRs and ion channels involved in respiratory disease and discuss advantages offered by antibodies as therapeutics at these targets. We highlight some recent GPCRs and ion channels linked to respiratory disease mechanisms and describe in detail recent progress made in the strategies for discovery of functional antibodies against challenging membrane protein targets such as GPCRs and ion channels. Copyright © 2016 Elsevier Inc. All rights reserved.

Photodissociation of ultracold diatomic strontium molecules with quantum state control.

PubMed

McDonald, M; McGuyer, B H; Apfelbeck, F; Lee, C-H; Majewska, I; Moszynski, R; Zelevinsky, T

2016-07-07

Chemical reactions at ultracold temperatures are expected to be dominated by quantum mechanical effects. Although progress towards ultracold chemistry has been made through atomic photoassociation, Feshbach resonances and bimolecular collisions, these approaches have been limited by imperfect quantum state selectivity. In particular, attaining complete control of the ground or excited continuum quantum states has remained a challenge. Here we achieve this control using photodissociation, an approach that encodes a wealth of information in the angular distribution of outgoing fragments. By photodissociating ultracold (88)Sr2 molecules with full control of the low-energy continuum, we access the quantum regime of ultracold chemistry, observing resonant and nonresonant barrier tunnelling, matter-wave interference of reaction products and forbidden reaction pathways. Our results illustrate the failure of the traditional quasiclassical model of photodissociation and instead are accurately described by a quantum mechanical model. The experimental ability to produce well-defined quantum continuum states at low energies will enable high-precision studies of long-range molecular potentials for which accurate quantum chemistry models are unavailable, and may serve as a source of entangled states and coherent matter waves for a wide range of experiments in quantum optics.

Organic molecules as sorbing tracers for the assessment of surface areas in consolidated aquifer systems

NASA Astrophysics Data System (ADS)

Schaffer, Mario; Warner, Wiebke; Kutzner, Susann; Börnick, Hilmar; Worch, Eckhard; Licha, Tobias

2017-03-01

Based on the assumption that the specific surface area to volume ratio Asurf/V of consolidated rock materials is proportional to the surface area available for sorption, several inorganic cations were recently proposed as sorbing (cation exchanging) tracers for estimating these ratios in aquifers (e.g., for deriving the efficient heat exchange area of geothermal reservoirs). The main disadvantages of inorganic ions, however, are the limited number of suitable ions, their potential geogenic background, and their challenging online detection at trace concentrations. In this work, the spectrum of chemical substances used as sorbing tracers expands by considering fluorescent organic compounds that are cationic. They have the advantage of being highly water soluble and easy to measure online at very low concentrations. Results from systematic lab column experiments with seven selected organic cations under various conditions (different salinities and temperatures) are presented, emphasizing the potential of organic molecules as alternative sorbing tracers especially in consolidated aquifer systems. This work is a first stepping stone in identifying suitable molecular structures that can be selected or even individually adapted to the requirements of the tracer tests and prevailing aquifer conditions.

Learning about Biomolecular Solvation from Water in Protein Crystals.

PubMed

Altan, Irem; Fusco, Diana; Afonine, Pavel V; Charbonneau, Patrick

2018-03-08

Water occupies typically 50% of a protein crystal and thus significantly contributes to the diffraction signal in crystallography experiments. Separating its contribution from that of the protein is, however, challenging because most water molecules are not localized and are thus difficult to assign to specific density peaks. The intricateness of the protein-water interface compounds this difficulty. This information has, therefore, not often been used to study biomolecular solvation. Here, we develop a methodology to surmount in part this difficulty. More specifically, we compare the solvent structure obtained from diffraction data for which experimental phasing is available to that obtained from constrained molecular dynamics (MD) simulations. The resulting spatial density maps show that commonly used MD water models are only partially successful at reproducing the structural features of biomolecular solvation. The radial distribution of water is captured with only slightly higher accuracy than its angular distribution, and only a fraction of the water molecules assigned with high reliability to the crystal structure is recovered. These differences are likely due to shortcomings of both the water models and the protein force fields. Despite these limitations, we manage to infer protonation states of some of the side chains utilizing MD-derived densities.

Fluorescence anisotropy (polarization): from drug screening to precision medicine

PubMed Central

Zhang, Hairong; Wu, Qian; Berezin, Mikhail Y.

2016-01-01

Introduction Fluorescence anisotropy (FA) is one of the major established methods accepted by industry and regulatory agencies for understanding the mechanisms of drug action and selecting drug candidates utilizing a high-throughput format. Areas covered This review covers the basics of FA and complementary methods, such as fluorescence lifetime anisotropy and their roles in the drug discovery process. The authors highlight the factors affecting FA readouts, fluorophore selection, and instrumentation. Furthermore, the authors describe the recent development of a successful, commercially valuable FA assay for Long QT syndrome drug toxicity to illustrate the role that FA can play in the early stages of drug discovery. Expert opinion Despite the success in drug discovery, the FA-based technique experiences competitive pressure from other homogeneous assays. That being said, FA is an established yet rapidly developing technique, recognized by academic institutions, the pharmaceutical industry, and regulatory agencies across the globe. The technical problems encountered in working with small molecules in homogeneous assays are largely solved, and new challenges come from more complex biological molecules and nanoparticles. With that, FA will remain one of the major work-horse techniques leading to precision (personalized) medicine. PMID:26289575

Exploring the role of water in molecular recognition: predicting protein ligandability using a combinatorial search of surface hydration sites.

PubMed

Vukovic, Sinisa; Brennan, Paul E; Huggins, David J

2016-09-01

The interaction between any two biological molecules must compete with their interaction with water molecules. This makes water the most important molecule in medicine, as it controls the interactions of every therapeutic with its target. A small molecule binding to a protein is able to recognize a unique binding site on a protein by displacing bound water molecules from specific hydration sites. Quantifying the interactions of these water molecules allows us to estimate the potential of the protein to bind a small molecule. This is referred to as ligandability. In the study, we describe a method to predict ligandability by performing a search of all possible combinations of hydration sites on protein surfaces. We predict ligandability as the summed binding free energy for each of the constituent hydration sites, computed using inhomogeneous fluid solvation theory. We compared the predicted ligandability with the maximum observed binding affinity for 20 proteins in the human bromodomain family. Based on this comparison, it was determined that effective inhibitors have been developed for the majority of bromodomains, in the range from 10 to 100 nM. However, we predict that more potent inhibitors can be developed for the bromodomains BPTF and BRD7 with relative ease, but that further efforts to develop inhibitors for ATAD2 will be extremely challenging. We have also made predictions for the 14 bromodomains with no reported small molecule K d values by isothermal titration calorimetry. The calculations predict that PBRM1(1) will be a challenging target, while others such as TAF1L(2), PBRM1(4) and TAF1(2), should be highly ligandable. As an outcome of this work, we assembled a database of experimental maximal K d that can serve as a community resource assisting medicinal chemistry efforts focused on BRDs. Effective prediction of ligandability would be a very useful tool in the drug discovery process.

Exploring the role of water in molecular recognition: predicting protein ligandability using a combinatorial search of surface hydration sites

NASA Astrophysics Data System (ADS)

Vukovic, Sinisa; Brennan, Paul E.; Huggins, David J.

2016-09-01

The interaction between any two biological molecules must compete with their interaction with water molecules. This makes water the most important molecule in medicine, as it controls the interactions of every therapeutic with its target. A small molecule binding to a protein is able to recognize a unique binding site on a protein by displacing bound water molecules from specific hydration sites. Quantifying the interactions of these water molecules allows us to estimate the potential of the protein to bind a small molecule. This is referred to as ligandability. In the study, we describe a method to predict ligandability by performing a search of all possible combinations of hydration sites on protein surfaces. We predict ligandability as the summed binding free energy for each of the constituent hydration sites, computed using inhomogeneous fluid solvation theory. We compared the predicted ligandability with the maximum observed binding affinity for 20 proteins in the human bromodomain family. Based on this comparison, it was determined that effective inhibitors have been developed for the majority of bromodomains, in the range from 10 to 100 nM. However, we predict that more potent inhibitors can be developed for the bromodomains BPTF and BRD7 with relative ease, but that further efforts to develop inhibitors for ATAD2 will be extremely challenging. We have also made predictions for the 14 bromodomains with no reported small molecule K d values by isothermal titration calorimetry. The calculations predict that PBRM1(1) will be a challenging target, while others such as TAF1L(2), PBRM1(4) and TAF1(2), should be highly ligandable. As an outcome of this work, we assembled a database of experimental maximal K d that can serve as a community resource assisting medicinal chemistry efforts focused on BRDs. Effective prediction of ligandability would be a very useful tool in the drug discovery process.

Electrospray deposition of organic molecules on bulk insulator surfaces.

PubMed

Hinaut, Antoine; Pawlak, Rémy; Meyer, Ernst; Glatzel, Thilo

2015-01-01

Large organic molecules are of important interest for organic-based devices such as hybrid photovoltaics or molecular electronics. Knowing their adsorption geometries and electronic structures allows to design and predict macroscopic device properties. Fundamental investigations in ultra-high vacuum (UHV) are thus mandatory to analyze and engineer processes in this prospects. With increasing size, complexity or chemical reactivity, depositing molecules by thermal evaporation becomes challenging. A recent way to deposit molecules in clean conditions is Electrospray Ionization (ESI). ESI keeps the possibility to work with large molecules, to introduce them in vacuum, and to deposit them on a large variety of surfaces. Here, ESI has been successfully applied to deposit triply fused porphyrin molecules on an insulating KBr(001) surface in UHV environment. Different deposition coverages have been obtained and characterization of the surface by in-situ atomic force microscopy working in the non-contact mode shows details of the molecular structures adsorbed on the surface. We show that UHV-ESI, can be performed on insulating surfaces in the sub-monolayer regime and to single molecules which opens the possibility to study a variety of complex molecules.

Exploiting the Bioactive Properties of the Dentin-Pulp Complex in Regenerative Endodontics.

PubMed

Smith, Anthony J; Duncan, Henry F; Diogenes, Anibal; Simon, Stephane; Cooper, Paul R

2016-01-01

The development of regenerative endodontic therapies offers exciting opportunities for future improvements in treatment outcomes. Advances in our understanding of regenerative events at the molecular and cellular levels are helping to underpin development of these therapies, although the various strategies differ in the translational challenges they pose. The identification of a variety of bioactive molecules, including growth factors, cytokines, chemokines, and matrix molecules, sequestered within dentin and dental pulp provides the opportunity to present key signaling molecules promoting reparative and regenerative events after injury. The protection of the biological activity of these molecules by mineral in dentin before their release allows a continuing supply of these molecules, while avoiding the short half-life and the non-human origin of exogenous molecules. The ready release of these bioactive molecules by the various tissue preparation agents, medicaments, and materials commonly used in endodontics highlights the opportunities for translational regenerative strategies exploiting these molecules with little change to existing clinical practice. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

The Challenging Experience Questionnaire: Characterization of challenging experiences with psilocybin mushrooms.

PubMed

Barrett, Frederick S; Bradstreet, Matthew P; Leoutsakos, Jeannie-Marie S; Johnson, Matthew W; Griffiths, Roland R

2016-12-01

Acute adverse psychological reactions to classic hallucinogens ("bad trips" or "challenging experiences"), while usually benign with proper screening, preparation, and support in controlled settings, remain a safety concern in uncontrolled settings (such as illicit use contexts). Anecdotal and case reports suggest potential adverse acute symptoms including affective (panic, depressed mood), cognitive (confusion, feelings of losing sanity), and somatic (nausea, heart palpitation) symptoms. Responses to items from several hallucinogen-sensitive questionnaires (Hallucinogen Rating Scale, the States of Consciousness Questionnaire, and the Five-Dimensional Altered States of Consciousness questionnaire) in an Internet survey of challenging experiences with the classic hallucinogen psilocybin were used to construct and validate a Challenging Experience Questionnaire. The stand-alone Challenging Experience Questionnaire was then validated in a separate sample. Seven Challenging Experience Questionnaire factors (grief, fear, death, insanity, isolation, physical distress, and paranoia) provide a phenomenological profile of challenging aspects of experiences with psilocybin. Factor scores were associated with difficulty, meaningfulness, spiritual significance, and change in well-being attributed to the challenging experiences. The factor structure did not differ based on gender or prior struggle with anxiety or depression. The Challenging Experience Questionnaire provides a basis for future investigation of predictors and outcomes of challenging experiences with classic hallucinogens. © The Author(s) 2016.

Fragment-based approaches to the discovery of kinase inhibitors.

PubMed

Mortenson, Paul N; Berdini, Valerio; O'Reilly, Marc

2014-01-01

Protein kinases are one of the most important families of drug targets, and aberrant kinase activity has been linked to a large number of disease areas. Although eminently targetable using small molecules, kinases present a number of challenges as drug targets, not least obtaining selectivity across such a large and relatively closely related target family. Fragment-based drug discovery involves screening simple, low-molecular weight compounds to generate initial hits against a target. These hits are then optimized to more potent compounds via medicinal chemistry, usually facilitated by structural biology. Here, we will present a number of recent examples of fragment-based approaches to the discovery of kinase inhibitors, detailing the construction of fragment-screening libraries, the identification and validation of fragment hits, and their optimization into potent and selective lead compounds. The advantages of fragment-based methodologies will be discussed, along with some of the challenges associated with using this route. Finally, we will present a number of key lessons derived both from our own experience running fragment screens against kinases and from a large number of published studies.

Scattering resonances in bimolecular collisions between NO radicals and H2 challenge the theoretical gold standard

NASA Astrophysics Data System (ADS)

Vogels, Sjoerd N.; Karman, Tijs; Kłos, Jacek; Besemer, Matthieu; Onvlee, Jolijn; van der Avoird, Ad; Groenenboom, Gerrit C.; van de Meerakker, Sebastiaan Y. T.

2018-02-01

Over the last 25 years, the formalism known as coupled-cluster (CC) theory has emerged as the method of choice for the ab initio calculation of intermolecular interaction potentials. The implementation known as CCSD(T) is often referred to as the gold standard in quantum chemistry. It gives excellent agreement with experimental observations for a variety of energy-transfer processes in molecular collisions, and it is used to calibrate density functional theory. Here, we present measurements of low-energy collisions between NO radicals and H2 molecules with a resolution that challenges the most sophisticated quantum chemistry calculations at the CCSD(T) level. Using hitherto-unexplored anti-seeding techniques to reduce the collision energy in a crossed-beam inelastic-scattering experiment, a resonance structure near 14 cm-1 is clearly resolved in the state-to-state integral cross-section, and a unique resonance fingerprint is observed in the corresponding differential cross-section. This resonance structure discriminates between two NO-H2 potentials calculated at the CCSD(T) level and pushes the required accuracy beyond the gold standard.

Analysis of Organic Anionic Surfactants in Fine and Coarse Fractions of Freshly Emitted Sea Spray Aerosol

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

Cochran, Richard E.; Laskina, Olga; Jayarathne, Thilina

The inclusion of organic compounds in freshly emitted sea spray aerosol (SSA) has been shown to be size-dependent, with an increasing organic fraction in smaller particles. Defining the molecular composition of sea spray aerosol has proven challenging, due to the mix of continental and background particles even in remote marine environments. Here we have used electrospray ionization-high resolution mass spectrometry in negative ion mode to identify organic compounds in nascent sea spray collected throughout a 25-day mesocosm experiment. Over 280 organic compounds from ten major homologous series were identified. These compounds were operationally defined as molecules containing a hydrophobic alkylmore » chain with a hydrophilic head group making them surface active. The most abundant class of molecules detected were saturated (C8–C24) and unsaturated (C12–C22) fatty acids. Fatty acid derivatives (including saturated oxo-fatty acids (C5–C18) and saturated hydroxy-fatty acids (C5–C18) were also identified. Interestingly, anthropogenic influences on SSA from the seawater were observed in the form of sulfate (C2–C7, C12–C17) and sulfonate (C16–C22) species. During the mesocosm, the distributions of molecules within each homologous series were observed to respond to variations among the levels of phytoplankton and bacteria in the seawater, indicating an important role of biological processes in determining the composition of SSA.« less

Drug-DNA interactions at single molecule level: A view with optical tweezers

NASA Astrophysics Data System (ADS)

Paramanathan, Thayaparan

Studies of small molecule--DNA interactions are essential for developing new drugs for challenging diseases like cancer and HIV. The main idea behind developing these molecules is to target and inhibit the reproduction of the tumor cells and infected cells. We mechanically manipulate single DNA molecule using optical tweezers to investigate two molecules that have complex and multiple binding modes. Mononuclear ruthenium complexes have been extensively studied as a test for rational drug design. Potential drug candidates should have high affinity to DNA and slow dissociation kinetics. To achieve this, motifs of the ruthenium complexes are altered. Our collaborators designed a dumb-bell shaped binuclear ruthenium complex that can only intercalate DNA by threading through its bases. Studying the binding properties of this complex in bulk studies took hours. By mechanically manipulating a single DNA molecule held with optical tweezers, we lower the barrier to thread and make it fast compared to the bulk experiments. Stretching single DNA molecules with different concentration of drug molecules and holding it at a constant force allows the binding to reach equilibrium. By this we can obtain the equilibrium fractional ligand binding and length of DNA at saturated binding. Fitting these results yields quantitative measurements of the binding thermodynamics and kinetics of this complex process. The second complex discussed in this study is Actinomycin D (ActD), a well studied anti-cancer agent that is used as a prototype for developing new generations of drugs. However, the biophysical basis of its activity is still unclear. Because ActD is known to intercalate double stranded DNA (dsDNA), it was assumed to block replication by stabilizing dsDNA in front of the replication fork. However, recent studies have shown that ActD binds with even higher affinity to imperfect duplexes and some sequences of single stranded DNA (ssDNA). We directly measure the on and off rates by stretching the DNA molecule to a certain force and holding it at constant force while adding the drug and then while washing off the drug. Our finding resolves the long lasting controversy of ActD binding modes, clearly showing that both the dsDNA binding and ssDNA binding converge to the same single mode. The result supports the hypothesis that the primary characteristic of ActD that contributes to its biological activity is its ability to inhibit cellular replication by binding to transcription bubbles and causing cell death.

Predicting human olfactory perception from chemical features of odor molecules.

PubMed

Keller, Andreas; Gerkin, Richard C; Guan, Yuanfang; Dhurandhar, Amit; Turu, Gabor; Szalai, Bence; Mainland, Joel D; Ihara, Yusuke; Yu, Chung Wen; Wolfinger, Russ; Vens, Celine; Schietgat, Leander; De Grave, Kurt; Norel, Raquel; Stolovitzky, Gustavo; Cecchi, Guillermo A; Vosshall, Leslie B; Meyer, Pablo

2017-02-24

It is still not possible to predict whether a given molecule will have a perceived odor or what olfactory percept it will produce. We therefore organized the crowd-sourced DREAM Olfaction Prediction Challenge. Using a large olfactory psychophysical data set, teams developed machine-learning algorithms to predict sensory attributes of molecules based on their chemoinformatic features. The resulting models accurately predicted odor intensity and pleasantness and also successfully predicted 8 among 19 rated semantic descriptors ("garlic," "fish," "sweet," "fruit," "burnt," "spices," "flower," and "sour"). Regularized linear models performed nearly as well as random forest-based ones, with a predictive accuracy that closely approaches a key theoretical limit. These models help to predict the perceptual qualities of virtually any molecule with high accuracy and also reverse-engineer the smell of a molecule. Copyright © 2017, American Association for the Advancement of Science.

Sensitivity and resolution in frequency comb spectroscopy of buffer gas cooled polyatomic molecules

NASA Astrophysics Data System (ADS)

Changala, P. Bryan; Spaun, Ben; Patterson, David; Doyle, John M.; Ye, Jun

2016-12-01

We discuss the use of cavity-enhanced direct frequency comb spectroscopy in the mid-infrared region with buffer gas cooling of polyatomic molecules for high-precision rovibrational absorption spectroscopy. A frequency comb coupled to an optical enhancement cavity allows us to collect high-resolution, broad-bandwidth infrared spectra of translationally and rotationally cold (10-20 K) gas-phase molecules with high absorption sensitivity and fast acquisition times. The design and performance of the combined apparatus are discussed in detail. Recorded rovibrational spectra in the CH stretching region of several organic molecules, including vinyl bromide (CH_2CHBr), adamantane (C_{10}H_{16}), and diamantane (C_{14}H_{20}) demonstrate the resolution and sensitivity of this technique, as well as the intrinsic challenges faced in extending the frontier of high-resolution spectroscopy to large complex molecules.

Magnetic fingerprint of individual Fe4 molecular magnets under compression by a scanning tunnelling microscope

NASA Astrophysics Data System (ADS)

Burgess, Jacob A. J.; Malavolti, Luigi; Lanzilotto, Valeria; Mannini, Matteo; Yan, Shichao; Ninova, Silviya; Totti, Federico; Rolf-Pissarczyk, Steffen; Cornia, Andrea; Sessoli, Roberta; Loth, Sebastian

2015-09-01

Single-molecule magnets (SMMs) present a promising avenue to develop spintronic technologies. Addressing individual molecules with electrical leads in SMM-based spintronic devices remains a ubiquitous challenge: interactions with metallic electrodes can drastically modify the SMM's properties by charge transfer or through changes in the molecular structure. Here, we probe electrical transport through individual Fe4 SMMs using a scanning tunnelling microscope at 0.5 K. Correlation of topographic and spectroscopic information permits identification of the spin excitation fingerprint of intact Fe4 molecules. Building from this, we find that the exchange coupling strength within the molecule's magnetic core is significantly enhanced. First-principles calculations support the conclusion that this is the result of confinement of the molecule in the two-contact junction formed by the microscope tip and the sample surface.

Giant Acceleration of Diffusion Observed in a Single-Molecule Experiment on F(1)-ATPase.

PubMed

Hayashi, Ryunosuke; Sasaki, Kazuo; Nakamura, Shuichi; Kudo, Seishi; Inoue, Yuichi; Noji, Hiroyuki; Hayashi, Kumiko

2015-06-19

The giant acceleration (GA) of diffusion is a universal phenomenon predicted by the theoretical analysis given by Reimann et al. [Phys. Rev. Lett. 87, 010602 (2001)]. Here we apply the theory of the GA of diffusion to a single-molecule experiment on a rotary motor protein, F(1), which is a component of F(o)F(1) adenosine triphosphate synthase. We discuss the energetic properties of F(1) and identify a high energy barrier of the rotary potential to be 20k(B)T, with the condition that the adenosine diphosphates are tightly bound to the F(1) catalytic sites. To conclude, the GA of diffusion is useful for measuring energy barriers in nonequilibrium and single-molecule experiments.

Giant Acceleration of Diffusion Observed in a Single-Molecule Experiment on F1-ATPase

NASA Astrophysics Data System (ADS)

Hayashi, Ryunosuke; Sasaki, Kazuo; Nakamura, Shuichi; Kudo, Seishi; Inoue, Yuichi; Noji, Hiroyuki; Hayashi, Kumiko

2015-06-01

The giant acceleration (GA) of diffusion is a universal phenomenon predicted by the theoretical analysis given by Reimann et al. [Phys. Rev. Lett. 87, 010602 (2001)]. Here we apply the theory of the GA of diffusion to a single-molecule experiment on a rotary motor protein, F1 , which is a component of Fo F1 adenosine triphosphate synthase. We discuss the energetic properties of F1 and identify a high energy barrier of the rotary potential to be 20 kBT , with the condition that the adenosine diphosphates are tightly bound to the F1 catalytic sites. To conclude, the GA of diffusion is useful for measuring energy barriers in nonequilibrium and single-molecule experiments.

MetaboID: a graphical user interface package for assignment of 1H NMR spectra of bodyfluids and tissues.

PubMed

MacKinnon, Neil; Somashekar, Bagganahalli S; Tripathi, Pratima; Ge, Wencheng; Rajendiran, Thekkelnaycke M; Chinnaiyan, Arul M; Ramamoorthy, Ayyalusamy

2013-01-01

Nuclear magnetic resonance based measurements of small molecule mixtures continues to be confronted with the challenge of spectral assignment. While multi-dimensional experiments are capable of addressing this challenge, the imposed time constraint becomes prohibitive, particularly with the large sample sets commonly encountered in metabolomic studies. Thus, one-dimensional spectral assignment is routinely performed, guided by two-dimensional experiments on a selected sample subset; however, a publicly available graphical interface for aiding in this process is currently unavailable. We have collected spectral information for 360 unique compounds from publicly available databases including chemical shift lists and authentic full resolution spectra, supplemented with spectral information for 25 compounds collected in-house at a proton NMR frequency of 900 MHz. This library serves as the basis for MetaboID, a Matlab-based user interface designed to aid in the one-dimensional spectral assignment process. The tools of MetaboID were built to guide resonance assignment in order of increasing confidence, starting from cursory compound searches based on chemical shift positions to analysis of authentic spike experiments. Together, these tools streamline the often repetitive task of spectral assignment. The overarching goal of the integrated toolbox of MetaboID is to centralize the one dimensional spectral assignment process, from providing access to large chemical shift libraries to providing a straightforward, intuitive means of spectral comparison. Such a toolbox is expected to be attractive to both experienced and new metabolomic researchers as well as general complex mixture analysts. Copyright © 2012 Elsevier Inc. All rights reserved.

Freezing-induced self-assembly of amphiphilic molecules

NASA Astrophysics Data System (ADS)

Albouy, P. A.; Deville, S.; Fulkar, A.; Hakouk, K.; Impéror-Clerc, M.; Klotz, M.; Liu, Q.; Marcellini, M.; Perez, J.

The self-assembly of amphiphilic molecules usually takes place in a liquid phase, near room temperature. Here, using small angle X-ray scattering (SAXS) experiments performed in real time, we show that freezing of aqueous solutions of copolymer amphiphilic molecules can induce self-assembly below 0{\\deg}C.

Freezing-induced self-assembly of amphiphilic molecules.

PubMed

Albouy, P A; Deville, S; Fulkar, A; Hakouk, K; Impéror-Clerc, M; Klotz, M; Liu, Q; Marcellini, M; Perez, J

2017-03-01

The self-assembly of amphiphilic molecules usually takes place in a liquid phase, near room temperature. Here, using small angle X-ray scattering (SAXS) experiments performed in real time, we show that freezing of aqueous solutions of copolymer amphiphilic molecules can induce self-assembly below 0 °C.

Zero-phonon-line emission of single molecules for applications in quantum information processing

NASA Astrophysics Data System (ADS)

Kiraz, Alper; Ehrl, M.; Mustecaplioglu, O. E.; Hellerer, T.; Brauchle, C.; Zumbusch, A.

2005-07-01

A single photon source which generates transform limited single photons is highly desirable for applications in quantum optics. Transform limited emission guarantees the indistinguishability of the emitted single photons. This, in turn brings groundbreaking applications in linear optics quantum information processing within an experimental reach. Recently, self-assembled InAs quantum dots and trapped atoms have successfully been demonstrated as such sources for highly indistinguishable single photons. Here, we demonstrate that nearly transform limited zero-phonon-line (ZPL) emission from single molecules can be obtained by using vibronic excitation. Furthermore we report the results of coincidence detection experiments at the output of a Michelson-type interferometer. These experiments reveal Hong-Ou-Mandel correlations as a proof of the indistinguishability of the single photons emitted consecutively from a single molecule. Therefore, single molecules constitute an attractive alternative to single InAs quantum dots and trapped atoms for applications in linear optics quantum information processing. Experiments were performed with a home-built confocal microscope keeping the sample in a superfluid liquid Helium bath at 1.4K. We investigated terrylenediimide (TDI) molecules highly diluted in hexadecane (Shpol'skii matrix). A continuous wave single mode dye laser was used for excitation of vibronic transitions of individual molecules. From the integral fluorescence, the ZPL of single molecules was selected with a spectrally narrow interference filter. The ZPL emission was then sent to a scanning Fabry-Perot interferometer for linewidth measurements or a Michelson-type interferometer for coincidence detection.

Enhanced cell uptake via non-covalent decollation of a single-walled carbon nanotube-DNA hybrid with polyethylene glycol-grafted poly(l-lysine) labeled with an Alexa-dye and its efficient uptake in a cancer cell

NASA Astrophysics Data System (ADS)

Fujigaya, Tsuyohiko; Yamamoto, Yuki; Kano, Arihiro; Maruyama, Atsushi; Nakashima, Naotoshi

2011-10-01

The use of single-walled carbon nanotubes (SWNTs) for biomedical applications is a promising approach due to their unique outer optical stimuli response properties, such as a photothermal response triggered by near-IR laser irradiation. The challenging task in order to realize such applications is to render the SWNTs biocompatible. For this purpose, the stable and homogeneous functionalization of the SWNTs with a molecule carrying a biocompatible group is very important. Here, we describe the design and synthesis of a polyanionic SWNT/DNA hybrid combined with a cationic poly(l-lysine) grafted by polyethylene glycol (PLL-g-PEG) to provide a supramolecular SWNT assembly. A titration experiment revealed that the assembly undergoes an approximately 1 : 1 reaction of the SWNT/DNA with PLL-g-PEG. We also found that SWNT/DNA is coated with PLL-g-PEG very homogeneously that avoids the non-specific binding of proteins on the SWNT surface. The experiment using the obtained supramolecular hybrid was carried out in vitro and a dramatic enhancement in the cell uptake efficiency compared to that of the SWNT/DNA hybrid without PLL-g-PEG was found.The use of single-walled carbon nanotubes (SWNTs) for biomedical applications is a promising approach due to their unique outer optical stimuli response properties, such as a photothermal response triggered by near-IR laser irradiation. The challenging task in order to realize such applications is to render the SWNTs biocompatible. For this purpose, the stable and homogeneous functionalization of the SWNTs with a molecule carrying a biocompatible group is very important. Here, we describe the design and synthesis of a polyanionic SWNT/DNA hybrid combined with a cationic poly(l-lysine) grafted by polyethylene glycol (PLL-g-PEG) to provide a supramolecular SWNT assembly. A titration experiment revealed that the assembly undergoes an approximately 1 : 1 reaction of the SWNT/DNA with PLL-g-PEG. We also found that SWNT/DNA is coated with PLL-g-PEG very homogeneously that avoids the non-specific binding of proteins on the SWNT surface. The experiment using the obtained supramolecular hybrid was carried out in vitro and a dramatic enhancement in the cell uptake efficiency compared to that of the SWNT/DNA hybrid without PLL-g-PEG was found. Electronic supplementary information (ESI) available: Additional absorption spectra, DLS plots and PL spectra. See DOI: 10.1039/c1nr10635j

Astrochemistry: Recent Advances in the Study of Carbon Molecules in Space

NASA Technical Reports Server (NTRS)

Salama, Farid

2006-01-01

Carbon molecules and ions play an important role in space. Polycyclic Aromatic Hydrocarbons (PAHs) are the best-known candidates to account for the infrared emission bands (UIR bands) and PAH spectral features are now being used as probes of the interstellar medium in Galactic and extra-galactic environments. PAHs are also thought to be among the carriers of the diffuse interstellar absorption bands (DIBs). In the model dealing with the interstellar spectral features, PAHs are present as a mixture of radicals, ions and neutral species. PAH ionization states reflect the ionization balance of the medium while PAH size, composition, and structure reflect the energetic and chemical history of the medium. A major challenge for laboratory Astrochemistry is to reproduce (in a realistic way) the physical conditions that exist in the emission and absorption interstellar zones. An extensive laboratory program has been developed in various laboratories to characterize the physical and chemical properties of PAHs in astrophysical environments and to describe how they influence the radiation and energy balance in space and the interstellar chemistry. In particular, laboratory experiments provide measurements of the spectral characteristics of interstellar PAH analogs from the ultraviolet and visible range to the infrared range for comparison with astronomical data. The harsh physical conditions of the interstellar medium - characterized by a low temperature, an absence of collisions and strong ultraviolet radiation fields - are simulated in the laboratory by associating a molecular beam with an ionizing discharge to generate a cold plasma expansion. PAH ions are formed from the neutral precursors in an isolated environment at low temperature (of the order of 100 K). The spectra of neutral and ionized PAHs are measured using the high sensitivity methods of cavity ring down spectroscopy (CRDS). These experiments provide unique information on the spectra of free, cold large carbon molecules and ions in the gas phase.

Simulating the VUV photochemistry of the upper atmosphere of Titan

NASA Astrophysics Data System (ADS)

Tigrine, Sarah; Carrasco, Nathalie; Vettier, Ludovic; Chitarra, Olivia; Cernogora, Guy

2016-10-01

The Cassini mission around Titan revealed that the interaction between the N2 and CH4 molecules and the solar VUV radiation leads to a complex chemistry above an altitude of 800km with the detection of heavy organic molecules like benzene (C6H6). This is consistent with an initiation of the aerosols in Titan's upper atmosphere. The presence of those molecules makes Titan a natural laboratory to witness and understand prebiotic-like chemistry but despite all the data collected, all the possible photochemical processes in such a hydrocarbon-nitrogen-rich environment are not precisely understood.This is why Titan's atmospheric chemistry experiments are of high interest, especially those focusing on the photochemistry as most of the Titan-like experiments are based on N2-CH4 plasma techniques. In order to reproduce this VUV photochemistry of N2 and CH4, we designed a photochemical reactor named APSIS which is to be coupled window-less with a VUV photon source as N2 needs wavelengths shorter than 100 nm in order to be dissociated. Those wavelengths are available at synchrotron beamlines but are challenging to obtain with common laboratory discharge lamps. At LATMOS, we developed a table-top VUV window-less source using noble gases for the micro-wave discharge. We started with Neon, as it has two resonance lines at 73.6 and 74.3 nm which allow us to dissociate and/or ionize both CH4 and N2.We will present here our first experimental results obtained with APSIS coupled with this VUV source. A range of different pressures below 1 mbar is tested, in parallel to different methane ratio. Moreover, other wavelengths are injected by adding some other noble gases in the MO discharge (He, Kr, Xe, Ar). We will review the mass spectra obtained in those different conditions and then discuss them regarding the Cassini data and other previous laboratory photochemical studies.

Experiments on the Dynamics of Molecular Processes: a Chronicle of Fifty Years

NASA Astrophysics Data System (ADS)

Boato, Giovanni; Volpi, Gian Gualberto

1999-10-01

This paper reviews the way in which, in the Italy of the years immediately after World War II, interest in the dynamics of molecular processes was awakened. The narrative begins with the work of a small number of chemists and physicists who, in the initial stage, interacted closely. In the course of the years, their interests diverged and younger people joined the newly formed groups. Even now, after half a century, a common approach can still to be seen regarding how to attack problems and perform experiments. Experimental work is discussed, bringing out the common viewpoint of fields as diverse as mass spectrometry, isotope effects, chemical kinetics, molecular beams, molecule-molecule interactions, molecule-ion interactions, molecule-surface interactions, and plasma chemistry.

Supramolecular Amino Acid Based Hydrogels: Probing the Contribution of Additive Molecules using NMR Spectroscopy

PubMed Central

Ramalhete, Susana M.; Nartowski, Karol P.; Sarathchandra, Nichola; Foster, Jamie S.; Round, Andrew N.; Angulo, Jesús

2017-01-01

Abstract Supramolecular hydrogels are composed of self‐assembled solid networks that restrict the flow of water. l‐Phenylalanine is the smallest molecule reported to date to form gel networks in water, and it is of particular interest due to its crystalline gel state. Single and multi‐component hydrogels of l‐phenylalanine are used herein as model materials to develop an NMR‐based analytical approach to gain insight into the mechanisms of supramolecular gelation. Structure and composition of the gel fibres were probed using PXRD, solid‐state NMR experiments and microscopic techniques. Solution‐state NMR studies probed the properties of free gelator molecules in an equilibrium with bound molecules. The dynamics of exchange at the gel/solution interfaces was investigated further using high‐resolution magic angle spinning (HR‐MAS) and saturation transfer difference (STD) NMR experiments. This approach allowed the identification of which additive molecules contributed in modifying the material properties. PMID:28401991

First-principles studies of electrical transport in nanoscale molecular junctions

NASA Astrophysics Data System (ADS)

Neaton, J. B.

2008-03-01

Understanding the conductance of individual molecular junctions is a forefront topic in theoretical nanoscience. The development of a general, efficient atomistic approach for treating an open system out of equilibrium with good accuracy, and then using it to inform experiment, is a significant open challenge in the field. Here I will describe studies where first-principles techniques, based on density functional theory (DFT) and beyond, are used to investigate some of the fundamental issues associated with single-molecule transport measurements. After a brief summary of previous work, a DFT-based scattering-state approach is presented and applied to H2 and amine-Au linked molecular junctions [1], two systems for which there exist reliable data [2]. Similar to most ab initio studies, we rely on a Landauer approach within DFT for junction conductance. Using this framework, which has proven relatively accurate for metallic point contacts, good agreement with experiment is obtained for the H2 conductance. For amine-Au linked junctions, however, the computed conductance is significantly larger than that measured,although structural trends are reproduced by the calculations. To explore this further, we draw on GW calculations of a prototypical metal-molecule contact, benzene on graphite, where interfacial polarization effects are found to drastically modify frontier orbital energies [3]. A physically motivated model self-energy correction is developed from our GW calculations,applied to the amine case, and shown to quantitatively explain the discrepancy with experiment. The importance of many-electron corrections beyond DFT for accurately computing molecular conductance and understanding experiments is thoroughly discussed. [1] S. Y. Quek et al., Nano Lett 7, 3482 (2007); K. H. Khoo et al., submitted (2007). [2] R. Smit et al., Nature 419, 906 (2002); L. Venkataraman et al., Nature 442 ,904 (2006). [3] J. B. Neaton et al., Phys. Rev. Lett. 97, 216405 (2006).

Monitoring an Induced Permafrost Warming Experiment Using ERT, Temperature, and NMR in Fairbanks, Alaska

NASA Astrophysics Data System (ADS)

Ulrich, C.; Ajo Franklin, J. B.; Ekblaw, I.; Lindsey, N.; Wagner, A. M.; Saari, S.; Daley, T. M.; Freifeld, B. M.

2016-12-01

As global temperatures continue to rise, permafrost landscapes will experience more rapid changes than other global climate zones. Permafrost thaw is a result of increased temperatures in arctic settings resulting in surface deformation and subsurface hydrology changes. From an engineering perspective, surface deformation poses a threat to the stability of existing infrastructure such as roads, utility piping, and building structures. Preemptively detecting or monitoring subsurface thaw dynamics presents a difficult challenge due to the long time scales as deformation occurs. Increased subsurface moisture content results from permafrost thaw of which electrical resistivity tomography (ERT), soil temperature, and nuclear magnetic resonance (NMR) are directly sensitive. In this experiment we evaluate spatial and temporal changes in subsurface permafrost conditions (moisture content and temperature) at a experimental heating plot in Fairbanks, AK. This study focuses on monitoring thaw signatures using multiple collocated electrical resistivity (ERT), borehole temperature, and borehole nuclear magnetic resonance (NMR) measurements. Timelapse ERT (sensitive to changes in moisture content) was inverted using collocated temperature and NMR to constrain ERT inversions. Subsurface thermal state was monitored with timelapse thermistors, sensitive to soil ice content. NMR was collected in multiple boreholes and is sensitive to changes in moisture content and pore scale distribution. As permafrost thaws more hydrogen, in the form of water, is available resulting in a changing NMR response. NMR requires the availability of liquid water in order to induce spin of the hydrogen molecule, hence, if frozen water molecules will be undetectable. In this study, the permafrost is poised close to 0oC and is mainly silt with small pore dimensions; this combination makes NMR particularly useful due to the possibility of sub-zero thaw conditions within the soil column. Overall this experiment presents a complementary suite of methods that provides feedback on subsurface permafrost state even in cases where soil texture might control unfrozen water content.

Cold molecules: Progress in quantum engineering of chemistry and quantum matter

NASA Astrophysics Data System (ADS)

Bohn, John L.; Rey, Ana Maria; Ye, Jun

2017-09-01

Cooling atoms to ultralow temperatures has produced a wealth of opportunities in fundamental physics, precision metrology, and quantum science. The more recent application of sophisticated cooling techniques to molecules, which has been more challenging to implement owing to the complexity of molecular structures, has now opened the door to the longstanding goal of precisely controlling molecular internal and external degrees of freedom and the resulting interaction processes. This line of research can leverage fundamental insights into how molecules interact and evolve to enable the control of reaction chemistry and the design and realization of a range of advanced quantum materials.

Single-molecule nanopore enzymology

PubMed Central

Wloka, Carsten; Maglia, Giovanni

2017-01-01

Biological nanopores are a class of membrane proteins that open nanoscale water-conduits in biological membranes. When they are reconstituted in artificial membranes and a bias voltage is applied across the membrane, the ionic current passing through individual nanopores can be used to monitor chemical reactions, to recognize individual molecules and, of most interest, to sequence DNA. More recently, proteins and enzymes have started being analysed with nanopores. Monitoring enzymatic reactions with nanopores, i.e. nanopore enzymology, has the unique advantage that it allows long-timescale observations of native proteins at the single-molecule level. Here we describe the approaches and challenges in nanopore enzymology. PMID:28630164

Molecular spintronics using single-molecule magnets

NASA Astrophysics Data System (ADS)

Bogani, Lapo; Wernsdorfer, Wolfgang

2008-03-01

A revolution in electronics is in view, with the contemporary evolution of the two novel disciplines of spintronics and molecular electronics. A fundamental link between these two fields can be established using molecular magnetic materials and, in particular, single-molecule magnets. Here, we review the first progress in the resulting field, molecular spintronics, which will enable the manipulation of spin and charges in electronic devices containing one or more molecules. We discuss the advantages over more conventional materials, and the potential applications in information storage and processing. We also outline current challenges in the field, and propose convenient schemes to overcome them.

Building block synthesis using the polymerase chain assembly method.

PubMed

Marchand, Julie A; Peccoud, Jean

2012-01-01

De novo gene synthesis allows the creation of custom DNA molecules without the typical constraints of traditional cloning assembly: scars, restriction site incompatibility, and the quest to find all the desired parts to name a few. Moreover, with the help of computer-assisted design, the perfect DNA molecule can be created along with its matching sequence ready to download. The challenge is to build the physical DNA molecules that have been designed with the software. Although there are several DNA assembly methods, this section presents and describes a method using the polymerase chain assembly (PCA).

Correlative Stochastic Optical Reconstruction Microscopy and Electron Microscopy

PubMed Central

Kim, Doory; Deerinck, Thomas J.; Sigal, Yaron M.; Babcock, Hazen P.; Ellisman, Mark H.; Zhuang, Xiaowei

2015-01-01

Correlative fluorescence light microscopy and electron microscopy allows the imaging of spatial distributions of specific biomolecules in the context of cellular ultrastructure. Recent development of super-resolution fluorescence microscopy allows the location of molecules to be determined with nanometer-scale spatial resolution. However, correlative super-resolution fluorescence microscopy and electron microscopy (EM) still remains challenging because the optimal specimen preparation and imaging conditions for super-resolution fluorescence microscopy and EM are often not compatible. Here, we have developed several experiment protocols for correlative stochastic optical reconstruction microscopy (STORM) and EM methods, both for un-embedded samples by applying EM-specific sample preparations after STORM imaging and for embedded and sectioned samples by optimizing the fluorescence under EM fixation, staining and embedding conditions. We demonstrated these methods using a variety of cellular targets. PMID:25874453

Materials by numbers: Computations as tools of discovery

PubMed Central

Landman, Uzi

2005-01-01

Current issues pertaining to theoretical simulations of materials, with a focus on systems of nanometer-scale dimensions, are discussed. The use of atomistic simulations as high-resolution numerical experiments, enabling and guiding formulation and testing of analytic theoretical descriptions, is demonstrated through studies of the generation and breakup of nanojets, which have led to the derivation of a stochastic hydrodynamic description. Subsequently, I illustrate the use of computations and simulations as tools of discovery, with examples that include the self-organized formation of nanowires, the surprising nanocatalytic activity of small aggregates of gold that, in the bulk form, is notorious for being chemically inert, and the emergence of rotating electron molecules in two-dimensional quantum dots. I conclude with a brief discussion of some key challenges in nanomaterials simulations. PMID:15870210

A magnetically focused molecular beam of ortho-water.

PubMed

Kravchuk, T; Reznikov, M; Tichonov, P; Avidor, N; Meir, Y; Bekkerman, A; Alexandrowicz, G

2011-01-21

Like dihydrogen, water exists as two spin isomers, ortho and para, with the nuclear magnetic moments of the hydrogen atoms either parallel or antiparallel. The ratio of the two spin isomers and their physical properties play an important role in a wide variety of research fields, ranging from astrophysics to nuclear magnetic resonance (NMR). Unlike ortho and para H(2), however, the two water isomers remain challenging to separate, and as a consequence, very little is currently known about their different physical properties. Here, we report the formation of a magnetically focused molecular beam of ortho-water. The beam we formed also had a particular spin projection. Thus, in the presence of holding magnetic fields, the water molecules are hyperpolarized, laying the foundation for ultrasensitive NMR experiments in the future.

Cosmic Carbon Chemistry: From the Interstellar Medium to the Early Earth

PubMed Central

Ehrenfreund, Pascale; Cami, Jan

2010-01-01

Astronomical observations have shown that carbonaceous compounds in the gas and solid state, refractory and icy are ubiquitous in our and distant galaxies. Interstellar molecular clouds and circumstellar envelopes are factories of complex molecular synthesis. A surprisingly large number of molecules that are used in contemporary biochemistry on Earth are found in the interstellar medium, planetary atmospheres and surfaces, comets, asteroids and meteorites, and interplanetary dust particles. In this article we review the current knowledge of abundant organic material in different space environments and investigate the connection between presolar and solar system material, based on observations of interstellar dust and gas, cometary volatiles, simulation experiments, and the analysis of extraterrestrial matter. Current challenges in astrochemistry are discussed and future research directions are proposed. PMID:20554702

Dendrimers in Medicine: Therapeutic Concepts and Pharmaceutical Challenges.

PubMed

Wu, Lin-Ping; Ficker, Mario; Christensen, Jørn B; Trohopoulos, Panagiotis N; Moghimi, Seyed Moein

2015-07-15

Dendrimers are three-dimensional macromolecular structures originating from a central core molecule and surrounded by successive addition of branching layers (generation). These structures exhibit a high degree of molecular uniformity, narrow molecular weight distribution, tunable size and shape characteristics, as well as multivalency. Collectively, these physicochemical characteristics together with advancements in design of biodegradable backbones have conferred many applications to dendrimers in formulation science and nanopharmaceutical developments. These have included the use of dendrimers as pro-drugs and vehicles for solubilization, encapsulation, complexation, delivery, and site-specific targeting of small-molecule drugs, biopharmaceuticals, and contrast agents. We briefly review these advances, paying particular attention to attributes that make dendrimers versatile for drug formulation as well as challenging issues surrounding the future development of dendrimer-based medicines.

Business of biosimilars - 14th annual conference (October 15-17, 2013 - Boston, Massachusetts, USA).

PubMed

Bourgoin, A

2013-12-01

Competition in the biological market offers a new set of opportunities and challenges within the healthcare industry. Biosimilars, like generic small-molecule drugs, can provide cost savings and increase patient access, while also promoting innovation. While large molecule manufacturers face many challenges unique to complex therapeutics, it is becoming clear that the commercialization of biosimilars shares many of the same hurdles as the generics market. The 14th Annual Business of Biosimilars Conference provided quality presentations from industry leaders regarding many commercial considerations for stakeholders interested in entering the biosimilars market. Opportunities to network with industry experts were offered, with over 120 attendees. Copyright 2013 Prous Science, S.A.U. or its licensors. All rights reserved.

Surface pressure field mapping using luminescent coatings

NASA Technical Reports Server (NTRS)

Mclachlan, B. G.; Kavandi, J. L.; Callis, J. B.; Gouterman, M.; Green, E.; Khalil, G.; Burns, D.

1993-01-01

In recent experiments we demonstrated the feasibility of using the oxygen dependence of luminescent molecules for surface pressure measurement in aerodynamic testing. This technique is based on the observation that for many luminescent molecules the light emitted increases as the oxygen partial pressure, and thus the air pressure, the molecules see decreases. In practice the surface to be observed is coated with an oxygen permeable polymer containing a luminescent molecule and illuminated with ultraviolet radiation. The airflow induced surface pressure field is seen as a luminescence intensity distribution which can be measured using quantitative video techniques. Computer processing converts the video data into a map of the surface pressure field. The experiments consisted of evaluating a trial luminescent coating in measuring the static surface pressure field over a two-dimensional NACA-0012 section model airfoil for Mach numbers ranging from 0.3 and 0.66. Comparison of the luminescent coating derived pressures were made to those obtained from conventional pressure taps. The method along with the experiment and its results will be described.

Investigations of electron helicity in optically active molecules using polarized beams of electrons and positrons

NASA Technical Reports Server (NTRS)

Gidley, D. W.; Rich, A.; Van House, J. C.; Zitzewitz, P. W.

1981-01-01

A positronium-formation experiment with a high sensitivity to a possible relation between the helicity of beta particles emitted in nuclear beta decay and the optical asymmetry of biological molecules is presented. The experiment is based on a mechanism in which the electrons in optically active molecules possess a helicity of less than 0.001, too weak to detect in radiolysis experiments, the sign of which depends on the chirality of the isomer. A helicity-dependent asymmetry is sought in the formation of the triplet ground state of positronium when a low-energy beam of polarized positrons of reversible helicity interacts with an optically active substance coating a channel electron multiplier. Asymmetries between positronium decays observed at positive and negative helicities for the same substance can thus be determined with a sensitivity of 0.0001, which represents a factor of 100 improvement over previous positronium experiments.

Observation of DNA Molecules Using Fluorescence Microscopy and Atomic Force Microscopy

ERIC Educational Resources Information Center

Ito, Takashi

2008-01-01

This article describes experiments for an undergraduate instrumental analysis laboratory that aim to observe individual double-stranded DNA (dsDNA) molecules using fluorescence microscopy and atomic force microscopy (AFM). dsDNA molecules are observed under several different conditions to discuss their chemical and physical properties. In…

Cobalt coated substrate for matrix-free analysis of small molecules by laser desorption/ionization mass spectrometry

NASA Astrophysics Data System (ADS)

Yalcin, Talat; Li, Liang

2009-12-01

Small molecule analysis is one of the most challenging issues in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. We have developed a cobalt coated substrate as a target for matrix-free analysis of small molecules in laser desorption/ionization mass spectrometry. Cobalt coating of 60-70 nm thickness has been characterized by scanning electron microscopy, energy dispersive X-ray analysis, X-ray diffraction, and laser induced breakdown spectroscopy. This target facilitates hundreds of samples to be spotted and analyzed without mixing any matrices, in a very short time. This can save a lot of time and money and can be a very practical approach for the analysis of small molecules by laser desorption/ionization mass spectrometry.

Quantitative analysis of single-molecule superresolution images

PubMed Central

Coltharp, Carla; Yang, Xinxing; Xiao, Jie

2014-01-01

This review highlights the quantitative capabilities of single-molecule localization-based superresolution imaging methods. In addition to revealing fine structural details, the molecule coordinate lists generated by these methods provide the critical ability to quantify the number, clustering, and colocalization of molecules with 10 – 50 nm resolution. Here we describe typical workflows and precautions for quantitative analysis of single-molecule superresolution images. These guidelines include potential pitfalls and essential control experiments, allowing critical assessment and interpretation of superresolution images. PMID:25179006

Free-standing few-layered graphene oxide films: selective, steady and lasting permeation of organic molecules with adjustable speeds

NASA Astrophysics Data System (ADS)

Huang, Tao; An, Qi; Luan, Xinglong; Zhang, Qian; Zhang, Yihe

2016-01-01

A variety of small molecules with diameters around 1 nm possess a range of functions, such as antibiotic, antimicrobic, anticoagulant, pesticidal and chemotherapy effects, making these molecules especially useful in various applications ranging from medical treatment to environmental microbiological control. However, the long-term steady delivery (release or permeation) of these small molecules with adjustable and controllable speeds has remained an especially challenging task. In this study, we prepared covalently cross-linked free-standing few-layered GO films using a layer-by-layer technique in combination with photochemical cross-linkages, and achieved a controlled release of positively charged, negatively charged, and zwitterionic small molecules with adjustable and controllable speeds. The steady delivery of the small molecule lasted up to 9 days. Other functionalities, such as graphene-enhanced Raman spectra and electrochemical properties that could also be integrated or employed in delivery systems, were also studied for our films. We expect the special molecular delivery properties of our films to lead to new possibilities in drug/fertilizer delivery and environmental microbiological control applications.A variety of small molecules with diameters around 1 nm possess a range of functions, such as antibiotic, antimicrobic, anticoagulant, pesticidal and chemotherapy effects, making these molecules especially useful in various applications ranging from medical treatment to environmental microbiological control. However, the long-term steady delivery (release or permeation) of these small molecules with adjustable and controllable speeds has remained an especially challenging task. In this study, we prepared covalently cross-linked free-standing few-layered GO films using a layer-by-layer technique in combination with photochemical cross-linkages, and achieved a controlled release of positively charged, negatively charged, and zwitterionic small molecules with adjustable and controllable speeds. The steady delivery of the small molecule lasted up to 9 days. Other functionalities, such as graphene-enhanced Raman spectra and electrochemical properties that could also be integrated or employed in delivery systems, were also studied for our films. We expect the special molecular delivery properties of our films to lead to new possibilities in drug/fertilizer delivery and environmental microbiological control applications. Electronic supplementary information (ESI) available: AFM images of GO and GO films, UV-vis spectra of delayed release, and permeation fidelities. See DOI: 10.1039/c5nr08129g

In Vitro Gluten Challenge Test for Celiac Disease Diagnosis.

PubMed

Khalesi, Maryam; Jafari, Seyed Ali; Kiani, Mohammadali; Picarelli, Antonio; Borghini, Raffaele; Sadeghi, Ramin; Eghtedar, Alireza; Ayatollahi, Hosein; Kianifar, Hamid R

2016-02-01

The in vitro gluten challenge test is an important diagnostic modality in celiac disease (CD), especially in patients who begin treatment with a gluten-free diet before adequate diagnostic workup or in cases with atypical CD. Available literature was reviewed regarding the accuracy of the in vitro gluten challenge test for CD diagnosis. MEDLINE, Scopus, and Google Scholar were searched, and studies that used serology and bowel biopsy as the criterion standard for diagnosis were included in our study. Data on authors, publication year, characteristics of the patient and control groups, patients' diet, duration of the gluten challenge test, histology findings, endomysial antibody (EMA) and anti-tissue transglutaminase (tTG) levels, CD markers, and intercellular cell adhesion molecule-1, and human leukocyte antigens before and after the gluten challenge test were extracted. Overall, 15 studies were included in this meta-analysis. Pooled sensitivity %/specificity % was 84/99 for EMA after the challenge, 52/96 for EMA without the challenge, 95.5/98.3 for anti-tTG after the challenge, and 95.1/98.3 for anti-tTG without the challenge test. Sensitivity/specificity for immunological markers were 89/97 for the percentage of CD25⁺-lamina propria lymphocytes, 96/91 for the percentage of CD3⁺-lamina propria lymphocytes, and 96.1/85.7 for the percentage of intercellular cell adhesion molecule-1-lamina propria lymphocytes. The factors that increased the sensitivity of EMA were longer test duration, and the evaluation of patients on a gluten-containing diet or short-term gluten-free diet. The in vitro gluten challenge test can be a useful part of the diagnostic workup of CD, rather than only a model to evaluate its mechanisms.

Planetary Organic Chemistry and the Origins of Biomolecules

PubMed Central

Benner, Steven A.; Kim, Hyo-Joong; Kim, Myung-Jung; Ricardo, Alonso

2010-01-01

Organic chemistry on a planetary scale is likely to have transformed carbon dioxide and reduced carbon species delivered to an accreting Earth. According to various models for the origin of life on Earth, biological molecules that jump-started Darwinian evolution arose via this planetary chemistry. The grandest of these models assumes that ribonucleic acid (RNA) arose prebiotically, together with components for compartments that held it and a primitive metabolism that nourished it. Unfortunately, it has been challenging to identify possible prebiotic chemistry that might have created RNA. Organic molecules, given energy, have a well-known propensity to form multiple products, sometimes referred to collectively as “tar” or “tholin.” These mixtures appear to be unsuited to support Darwinian processes, and certainly have never been observed to spontaneously yield a homochiral genetic polymer. To date, proposed solutions to this challenge either involve too much direct human intervention to satisfy many in the community, or generate molecules that are unreactive “dead ends” under standard conditions of temperature and pressure. Carbohydrates, organic species having carbon, hydrogen, and oxygen atoms in a ratio of 1:2:1 and an aldehyde or ketone group, conspicuously embody this challenge. They are components of RNA and their reactivity can support both interesting spontaneous chemistry as part of a “carbohydrate world,” but they also easily form mixtures, polymers and tars. We describe here the latest thoughts on how on this challenge, focusing on how it might be resolved using minerals containing borate, silicate, and molybdate, inter alia. PMID:20504964

Exploring the feasibility of an anti-idiotypic cocaine vaccine: analysis of the specificity of anticocaine antibodies (Ab1) capable of inducing Ab2beta anti-idiotypic antibodies.

PubMed

Schabacker, D S; Kirschbaum, K S; Segre, M

2000-05-01

Conventional vaccination with the cocaine molecule conjugated to a protein carrier is a new approach in the treatment of addiction. Experimentally, this strategy has been shown to alter the pharmacokinetics as well as the psychostimulant effect of a cocaine challenge. The purpose of this study was to investigate whether a more stable and less controversial molecule, an anti-idiotypic antibody, which mimics the configuration of the cocaine molecule (Ab2beta), could be successfully used instead of cocaine. Two cocaine conjugates that presented different areas of the cocaine molecule to the immune system were used to produce monoclonal antibodies specific for cocaine (Ab1). Several anti-idiotypic antibodies were then produced. Four were identified as Ab2beta, or internal images of the antigen; when injected into BALB/c mice, they elicited an anticocaine response. The anticocaine response elicited by one of the four Ab2beta (K1-4c) was sufficient to significantly reduce the level of cocaine that targeted the brain following cocaine challenge, compared with the level of cocaine found in the brain of control animals immunized with irrelevant antibody. In conclusion, the possibility of an anti-idiotypic vaccine seems to be worth pursuing.

One-Shot Determination of Residual Dipolar Couplings: Application to the Structural Discrimination of Small Molecules Containing Multiple Stereocenters.

PubMed

Castañar, Laura; Garcia, Manuela; Hellemann, Erich; Nolis, Pau; Gil, Roberto R; Parella, Teodor

2016-11-18

A novel approach for the fast and efficient structural discrimination of molecules containing multiple stereochemical centers is described. A robust J-resolved HSQC experiment affording highly resolved 1 J CH / 1 T CH splittings along the indirect dimension and homodecoupled 1 H signals in the detected dimension is proposed. The experiment enables in situ distinction of both isotropic and anisotropic components of molecules dissolved in compressed PMMA gels, allowing a rapid and direct one-shot determination of accurate residual dipolar coupling constants from a single NMR spectrum.

Stoichiometry of the Cre recombinase bound to the lox recombining site.

PubMed Central

Mack, A; Sauer, B; Abremski, K; Hoess, R

1992-01-01

The site-specific recombinase Cre from bacteriophage P1 binds and carries out recombination at a 34 bp lox site. The lox site consists of two 13 bp inverted repeats, separated by an 8 bp spacer region. Both the palindromic nature of the site and the results of footprinting and band shift experiments suggest that a minimum of two Cre molecules bind to a lox site. We report here experiments that demonstrate the absolute stoichiometry of the Cre-lox complex to be one molecule of Cre bound per inverted repeat, or two molecules per lox site. Images PMID:1408747

A mechanical model of bacteriophage DNA ejection

NASA Astrophysics Data System (ADS)

Arun, Rahul; Ghosal, Sandip

2017-08-01

Single molecule experiments on bacteriophages show an exponential scaling for the dependence of mobility on the length of DNA within the capsid. It has been suggested that this could be due to the ;capstan mechanism; - the exponential amplification of friction forces that result when a rope is wound around a cylinder as in a ship's capstan. Here we describe a desktop experiment that illustrates the effect. Though our model phage is a million times larger, it exhibits the same scaling observed in single molecule experiments.

DNA origami as biocompatible surface to match single-molecule and ensemble experiments

PubMed Central

Gietl, Andreas; Holzmeister, Phil; Grohmann, Dina; Tinnefeld, Philip

2012-01-01

Single-molecule experiments on immobilized molecules allow unique insights into the dynamics of molecular machines and enzymes as well as their interactions. The immobilization, however, can invoke perturbation to the activity of biomolecules causing incongruities between single molecule and ensemble measurements. Here we introduce the recently developed DNA origami as a platform to transfer ensemble assays to the immobilized single molecule level without changing the nano-environment of the biomolecules. The idea is a stepwise transfer of common functional assays first to the surface of a DNA origami, which can be checked at the ensemble level, and then to the microscope glass slide for single-molecule inquiry using the DNA origami as a transfer platform. We studied the structural flexibility of a DNA Holliday junction and the TATA-binding protein (TBP)-induced bending of DNA both on freely diffusing molecules and attached to the origami structure by fluorescence resonance energy transfer. This resulted in highly congruent data sets demonstrating that the DNA origami does not influence the functionality of the biomolecule. Single-molecule data collected from surface-immobilized biomolecule-loaded DNA origami are in very good agreement with data from solution measurements supporting the fact that the DNA origami can be used as biocompatible surface in many fluorescence-based measurements. PMID:22523083

Perinatal programming of emotional brain circuits: an integrative view from systems to molecules

PubMed Central

Bock, Jörg; Rether, Kathy; Gröger, Nicole; Xie, Lan; Braun, Katharina

2014-01-01

Environmental influences such as perinatal stress have been shown to program the developing organism to adapt brain and behavioral functions to cope with daily life challenges. Evidence is now accumulating that the specific and individual effects of early life adversity on the functional development of brain and behavior emerge as a function of the type, intensity, timing and the duration of the adverse environment, and that early life stress (ELS) is a major risk factor for developing behavioral dysfunctions and mental disorders. Results from clinical as well as experimental studies in animal models support the hypothesis that ELS can induce functional “scars” in prefrontal and limbic brain areas, regions that are essential for emotional control, learning and memory functions. On the other hand, the concept of “stress inoculation” is emerging from more recent research, which revealed positive functional adaptations in response to ELS resulting in resilience against stress and other adversities later in life. Moreover, recent studies indicate that early life experiences and the resulting behavioral consequences can be transmitted to the next generation, leading to a transgenerational cycle of adverse or positive adaptations of brain function and behavior. In this review we propose a unifying view of stress vulnerability and resilience by connecting genetic predisposition and programming sensitivity to the context of experience-expectancy and transgenerational epigenetic traits. The adaptive maturation of stress responsive neural and endocrine systems requires environmental challenges to optimize their functions. Repeated environmental challenges can be viewed within the framework of the match/mismatch hypothesis, the outcome, psychopathology or resilience, depends on the respective predisposition and on the context later in life. PMID:24550772

Measurements of trap dynamics of cold OH molecules using resonance-enhanced multiphoton ionization

NASA Astrophysics Data System (ADS)

Gray, John M.; Bossert, Jason A.; Shyur, Yomay; Lewandowski, H. J.

2017-08-01

Trapping cold, chemically important molecules with electromagnetic fields is a useful technique to study small molecules and their interactions. Traps provide long interaction times, which are needed to precisely examine these low-density molecular samples. However, the trapping fields lead to nonuniform molecular density distributions in these systems. Therefore, it is important to be able to experimentally characterize the spatial density distribution in the trap. Ionizing molecules at different locations in the trap using resonance-enhanced multiphoton ionization (REMPI) and detecting the resulting ions can be used to probe the density distribution even at the low density present in these experiments because of the extremely high efficiency of detection. Until recently, one of the most chemically important molecules, OH, did not have a convenient REMPI scheme identified. Here, we use a newly developed 1 +1' REMPI scheme to detect trapped cold OH molecules. We use this capability to measure the trap dynamics of the central density of the cloud and the density distribution. These types of measurements can be used to optimize loading of molecules into traps, as well as to help characterize the energy distribution, which is critical knowledge for interpreting molecular collision experiments.

ChemBank: a small-molecule screening and cheminformatics resource database.

PubMed

Seiler, Kathleen Petri; George, Gregory A; Happ, Mary Pat; Bodycombe, Nicole E; Carrinski, Hyman A; Norton, Stephanie; Brudz, Steve; Sullivan, John P; Muhlich, Jeremy; Serrano, Martin; Ferraiolo, Paul; Tolliday, Nicola J; Schreiber, Stuart L; Clemons, Paul A

2008-01-01

ChemBank (http://chembank.broad.harvard.edu/) is a public, web-based informatics environment developed through a collaboration between the Chemical Biology Program and Platform at the Broad Institute of Harvard and MIT. This knowledge environment includes freely available data derived from small molecules and small-molecule screens and resources for studying these data. ChemBank is unique among small-molecule databases in its dedication to the storage of raw screening data, its rigorous definition of screening experiments in terms of statistical hypothesis testing, and its metadata-based organization of screening experiments into projects involving collections of related assays. ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules. Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the Broad Institute by collaborators from the worldwide research community. The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.

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.

Tuned range separated hybrid functionals for solvated low bandgap oligomers

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

Queiroz, Thiago B. de, E-mail: thiago.branquinho-de-queiroz@uni-bayreuth.de; Kümmel, Stephan

2015-07-21

The description of charge transfer excitations has long been a challenge to time dependent density functional theory. The recently developed concept of “optimally tuned range separated hybrid (OT-RSH) functionals” has proven to describe charge transfer excitations accurately in many cases. However, describing solvated or embedded systems is yet a challenge. This challenge is not only computational but also conceptual, because the tuning requires identifying a specific orbital, typically the highest occupied one of the molecule under study. For solvated molecules, this orbital may be delocalized over the solvent. We here demonstrate that one way of overcoming this problem is tomore » use a locally projected self-consistent field diagonalization on an absolutely localized molecular orbital expansion. We employ this approach to determine ionization energies and the optical gap of solvated oligothiophenes, i.e., paradigm low gap systems that are of relevance in organic electronics. Dioxane solvent molecules are explicitly represented in our calculations, and the ambiguities of straightforward parameter tuning in solution are elucidated. We show that a consistent estimate of the optimal range separated parameter (ω) at the limit of bulk solvation can be obtained by gradually extending the solvated system. In particular, ω is influenced by the solvent beyond the first coordination sphere. For determining ionization energies, a considerable number of solvent molecules on the first solvation shell must be taken into account. We demonstrate that accurately calculating optical gaps of solvated systems using OT-RSH can be done in three steps: (i) including the chemical environment when determining the range-separation parameter, (ii) taking into account the screening due to the solvent, and (iii) using realistic molecular geometries.« less

Direct photoassociation of halo molecules in ultracold 86 Sr

NASA Astrophysics Data System (ADS)

Aman, J. A.; Hill, Joshua; Killian, T. C.

2017-04-01

We investigate the creation of 1S0 +1S0 halo molecules in strontium 86 through direct photoassociation in an optical dipole trap. We drive two photon Raman transitions near-resonance with a molecular level of the 1S0 +3P1 interatomic potential as the intermediate state. This provides large Frank-Condon factors and allows us to observe resonances for the creation of halo molecules through higher order Raman processes. The halo molecule is bound by EB 85 kHz at low excitation-laser intensity, but experiments show large AC Stark shifts of the molecular binding energy. These conditions suggest that STIRAP should be very effective for improving molecular conversion efficiency. Further experiments in a 3D lattice will explore molecular lifetimes and collision rates. Travel support provided by Shell Corporation.

Decomposition of energetic molecules by interfacing with a catalytic oxide: opportunities and challenges

NASA Astrophysics Data System (ADS)

Wang, Fenggong; Tsyshevsky, Roman; Zverev, Anton; Mitrofanov, Anatoly; Kuklja, Maija

Organic-inorganic interfaces provide both intrigues and opportunities for designing systems that possess properties and functionalities inaccessible by each individual component. In particular, mixing with a photocatalyst may significantly affect the adsorption, decomposition, and photoresponse of organic molecules. Here, we choose the formulation of TiO2 and trinitrotoluene (TNT), a highly catalytic oxide and a prominent explosive, as a prototypical example to explore the interaction at the interface on the photosensitivity of energetic materials. We show that, whether or not a catalytic oxide additive can help molecular decompositions under light illumination depends largely on the band alignment between the oxide surface and the energetic molecule. Furthermore, an oxygen vacancy can lead to the electron density transfer from the surface to the energetic molecules, causing an enhancement of the bonding between molecules and surface and a reduction of the molecular decomposition activation barriers.

Treatment of Gram-negative bacterial infections by potentiation of antibiotics.

PubMed

Zabawa, Thomas P; Pucci, Michael J; Parr, Thomas R; Lister, Troy

2016-10-01

Infections caused by antibiotic-resistant pathogens, particularly Gram-negative bacteria, represent significant treatment challenges for physicians resulting in high rates of morbidity and mortality. The outer membrane of Gram-negative bacteria acts as a permeability barrier to many compounds that would otherwise be effective antibacterial agents, including those effective against Gram-positive pathogens. Potentiator molecules disrupt this barrier allowing entry of otherwise impermeant molecules, thus providing a strategy to render multi-drug resistant pathogens susceptible to a broader range of antibiotics. Potentiator molecules are cationic and the mechanism of disruption involves interaction with the negatively charged outer membrane. This physical attribute, along with an often high degree of lipophilicity typically endears these molecules with unacceptable toxicity. Presented herein are examples of advanced potentiator molecules being evaluated for use in combination therapy for the treatment of resistant Gram-negative infections. Copyright © 2016 Elsevier Ltd. All rights reserved.

Porous materials with pre-designed single-molecule traps for CO2 selective adsorption

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

Li, JR; Yu, JM; Lu, WG

2013-02-26

Despite tremendous efforts, precise control in the synthesis of porous materials with pre-designed pore properties for desired applications remains challenging. Newly emerged porous metal-organic materials, such as metal-organic polyhedra and metal-organic frameworks, are amenable to design and property tuning, enabling precise control of functionality by accurate design of structures at the molecular level. Here we propose and validate, both experimentally and computationally, a precisely designed cavity, termed a 'single-molecule trap', with the desired size and properties suitable for trapping target CO2 molecules. Such a single-molecule trap can strengthen CO2-host interactions without evoking chemical bonding, thus showing potential for CO2 capture.more » Molecular single-molecule traps in the form of metal-organic polyhedra are designed, synthesised and tested for selective adsorption of CO2 over N-2 and CH4, demonstrating the trapping effect. Building these pre-designed single-molecule traps into extended frameworks yields metal-organic frameworks with efficient mass transfer, whereas the CO2 selective adsorption nature of single-molecule traps is preserved.« less

Site-Selection in Single-Molecule Junction for Highly Reproducible Molecular Electronics.

PubMed

Kaneko, Satoshi; Murai, Daigo; Marqués-González, Santiago; Nakamura, Hisao; Komoto, Yuki; Fujii, Shintaro; Nishino, Tomoaki; Ikeda, Katsuyoshi; Tsukagoshi, Kazuhito; Kiguchi, Manabu

2016-02-03

Adsorption sites of molecules critically determine the electric/photonic properties and the stability of heterogeneous molecule-metal interfaces. Then, selectivity of adsorption site is essential for development of the fields including organic electronics, catalysis, and biology. However, due to current technical limitations, site-selectivity, i.e., precise determination of the molecular adsorption site, remains a major challenge because of difficulty in precise selection of meaningful one among the sites. We have succeeded the single site-selection at a single-molecule junction by performing newly developed hybrid technique: simultaneous characterization of surface enhanced Raman scattering (SERS) and current-voltage (I-V) measurements. The I-V response of 1,4-benzenedithiol junctions reveals the existence of three metastable states arising from different adsorption sites. Notably, correlated SERS measurements show selectivity toward one of the adsorption sites: "bridge sites". This site-selectivity represents an essential step toward the reliable integration of individual molecules on metallic surfaces. Furthermore, the hybrid spectro-electric technique reveals the dependence of the SERS intensity on the strength of the molecule-metal interaction, showing the interdependence between the optical and electronic properties in single-molecule junctions.

Therapeutic approaches to preventing cell death in Huntington disease

PubMed Central

Kaplan, Anna; Stockwell, Brent R.

2012-01-01

Neurodegenerative diseases affect the lives of millions of patients and their families. Due to the complexity of these diseases and our limited understanding of their pathogenesis, the design of therapeutic agents that can effectively treat these diseases has been challenging. Huntington disease (HD) is one of several neurological disorders with few therapeutic options. HD, like numerous other neurodegenerative diseases, involves extensive neuronal cell loss. One potential strategy to combat HD and other neurodegenerative disorders is to intervene in the execution of neuronal cell death. Inhibiting neuronal cell death pathways may slow the development of neurodegeneration. However, discovering small molecule inhibitors of neuronal cell death remains a significant challenge. Here, we review candidate therapeutic targets controlling cell death mechanisms that have been the focus of research in HD, as well as an emerging strategy that has been applied to developing small molecule inhibitors—fragment-based drug discovery (FBDD). FBDD has been successfully used in both industry and academia to identify selective and potent small molecule inhibitors, with a focus on challenging proteins that are not amenable to traditional high-throughput screening approaches. FBDD has been used to generate potent leads, pre-clinical candidates, and has led to the development of an FDA approved drug. This approach can be valuable for identifying modulators of cell-death-regulating proteins; such compounds may prove to be the key to halting the progression of HD and other neurodegenerative disorders. PMID:22967354

The AMINO experiment: exposure of amino acids in the EXPOSE-R experiment on the International Space Station and in laboratory

NASA Astrophysics Data System (ADS)

Bertrand, Marylène; Chabin, Annie; Colas, Cyril; Cadène, Martine; Chaput, Didier; Brack, Andre; Cottin, Herve

2015-01-01

In order to confirm the results of previous experiments concerning the chemical behaviour of organic molecules in the space environment, organic molecules (amino acids and a dipeptide) in pure form and embedded in meteorite powder were exposed in the AMINO experiment in the EXPOSE-R facility onboard the International Space Station. After exposure to space conditions for 24 months (2843 h of irradiation), the samples were returned to the Earth and analysed in the laboratory for reactions caused by solar ultraviolet (UV) and other electromagnetic radiation. Laboratory UV exposure was carried out in parallel in the Cologne DLR Center (Deutsches Zentrum für Luft und Raumfahrt). The molecules were extracted from the sample holder and then (1) derivatized by silylation and analysed by gas chromatography coupled to a mass spectrometer (GC-MS) in order to quantify the rate of degradation of the compounds and (2) analysed by high-resolution mass spectrometry (HRMS) in order to understand the chemical reactions that occurred. The GC-MS results confirm that resistance to irradiation is a function of the chemical nature of the exposed molecules and of the wavelengths of the UV light. They also confirm the protective effect of a coating of meteorite powder. The most altered compounds were the dipeptides and aspartic acid while the most robust were compounds with a hydrocarbon chain. The MS analyses document the products of reactions, such as decarboxylation and decarbonylation of aspartic acid, taking place after UV exposure. Given the universality of chemistry in space, our results have a broader implication for the fate of organic molecules that seeded the planets as soon as they became habitable as well as for the effects of UV radiation on exposed molecules at the surface of Mars, for example.

Electrophoretic extraction of low molecular weight cationic analytes from sodium dodecyl sulfate containing sample matrices for their direct electrospray ionization mass spectrometry.

PubMed

Kinde, Tristan F; Lopez, Thomas D; Dutta, Debashis

2015-03-03

While the use of sodium dodecyl sulfate (SDS) in separation buffers allows efficient analysis of complex mixtures, its presence in the sample matrix is known to severely interfere with the mass-spectrometric characterization of analyte molecules. In this article, we report a microfluidic device that addresses this analytical challenge by enabling inline electrospray ionization mass spectrometry (ESI-MS) of low molecular weight cationic samples prepared in SDS containing matrices. The functionality of this device relies on the continuous extraction of analyte molecules into an SDS-free solvent stream based on the free-flow zone electrophoresis (FFZE) technique prior to their ESI-MS analysis. The reported extraction was accomplished in our current work in a glass channel with microelectrodes fabricated along its sidewalls to realize the desired electric field. Our experiments show that a key challenge to successfully operating such a device is to suppress the electroosmotically driven fluid circulations generated in its extraction channel that otherwise tend to vigorously mix the liquid streams flowing through this duct. A new coating medium, N-(2-triethoxysilylpropyl) formamide, recently demonstrated by our laboratory to nearly eliminate electroosmotic flow in glass microchannels was employed to address this issue. Applying this surface modifier, we were able to efficiently extract two different peptides, human angiotensin I and MRFA, individually from an SDS containing matrix using the FFZE method and detect them at concentrations down to 3.7 and 6.3 μg/mL, respectively, in samples containing as much as 10 mM SDS. Notice that in addition to greatly reducing the amount of SDS entering the MS instrument, the reported approach allows rapid solvent exchange for facilitating efficient analyte ionization desired in ESI-MS analysis.

Fluorine-18 labeled tracers for PET studies in the neurosciences

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

Ding, Yu-Shin; Fowler, J.S.

This chapter focuses on fluorine-18, the positron emitter with the longest half-life, the lowest positron energy and probably, the most challenging chemistry. The incorporation of F-18 into organic compounds presents many challenges, including: the need to synthesize and purify the compound within a 2--3 hour time frame; the limited number of labeled precursor molecules; the need to work on a microscale; and the need to produce radiotracers which are chemically and radiochemically pure, sterile and pyrogen-free, and suitable for intravenous injection. The PET method and F-18 labeling of organic molecules are described followed by highlights of the applications of F-18more » labeled compounds in the neurosciences and neuropharmacology. It is important to emphasize the essential and pivotal role that organic synthesis has played in the progression of the PET field over the past twenty years from one in which only a handful of institutions possessed the instrumentation and staff to carry out research to the present-day situation where there are more than 200 PET centers worldwide. During this period PET has become an important scientific tool in the neurosciences, cardiology and oncology. It is important to point out that PET is by no means a mature field. The fact that a hundreds of different F-18 labeled compounds have been developed but only a few possess the necessary selectivity and sensitivity in vivo to track a specific biochemical process illustrates this and underscores a major difficulty in radiotracer development, namely the selection of priority structures for synthesis and the complexities of the interactions between chemical compounds and living systems. New developments in rapid organic synthesis are needed in order to investigate new molecular targets and to improve the quantitative nature of PET experiments.« less

Mapping the Small Molecule Interactome by Mass Spectrometry.

PubMed

Flaxman, Hope A; Woo, Christina M

2018-01-16

Mapping small molecule interactions throughout the proteome provides the critical structural basis for functional analysis of their impact on biochemistry. However, translation of mass spectrometry-based proteomics methods to directly profile the interaction between a small molecule and the whole proteome is challenging because of the substoichiometric nature of many interactions, the diversity of covalent and noncovalent interactions involved, and the subsequent computational complexity associated with their spectral assignment. Recent advances in chemical proteomics have begun fill this gap to provide a structural basis for the breadth of small molecule-protein interactions in the whole proteome. Innovations enabling direct characterization of the small molecule interactome include faster, more sensitive instrumentation coupled to chemical conjugation, enrichment, and labeling methods that facilitate detection and assignment. These methods have started to measure molecular interaction hotspots due to inherent differences in local amino acid reactivity and binding affinity throughout the proteome. Measurement of the small molecule interactome is producing structural insights and methods for probing and engineering protein biochemistry. Direct structural characterization of the small molecule interactome is a rapidly emerging area pushing new frontiers in biochemistry at the interface of small molecules and the proteome.

Performance and Shock Sensitivity Evaluations of Reduced Sensitivity Explosives

NASA Astrophysics Data System (ADS)

Bowden, Patrick; Tappan, Bryce; Schmitt, Matthew; Lichthardt, Joseph; Hill, Larry

2017-06-01

Making high explosives that possess insensitivity on par with TATB-based plastic bonded explosives (PBXs), while outperforming them, has proven to be a difficult challenge. Many molecules that have challenged TATB have fallen short in either small-scale sensitivity (impact, friction), thermal stability, or possessing a shock sensitivity that is either too high or too low. Recently, an alternative approach to single-molecule-based PBXs has been blending and/or co-crystallizing explosive molecules to address shortcomings of individual components. With this approach in mind, formulations have been prepared containing 1,1-diamino-2,2-dinitroethene (DADNE or FOX-7) or 3,3'-diamino-4,4'-azoxyfurazan (DAAF) with 3-nitro-1,2,4-triazole-5-one (NTO). Detailed characterization of these mixtures has been described in a concurrent study. Here we focus on in depth performance metrics such as cylinder wall expansion and CJ pressure (via free surface velocity) and shock sensitivity, by small-scale gap-testing, were investigated as a function of weight percentages of the components. Results will be contrasted with known insensitive high explosives.

Round table part 4: Identification of the key technologies and collaboration for Food production and preparation

NASA Astrophysics Data System (ADS)

Lasseur, Christophe; Tikhomirov, Alexander A.; Wheeler, Raymond

2016-07-01

Although the two first metabolic needs are based on simple molecule (i.e. oxygen and water), the third metabolic needs considered a tremendously large number and diversity of molecules: food. Today, physical chemical technologies do not allow to synthetize all the spectrum of molecules and biological processes have to be considered. Moreover, the raw material products by plants or by microorganisms are generally not directly edible or palatable and would need either transformation, assembly and/or storage. In other words the challenges of the food cannot be reduced to the plant production but need to include as well the complete chain, from the production conditions and the biomass quality up to the final edible products and its acceptance. In other words all the steps have to be considered and characterize. Today these challenges requires a high level of plants characterization. This round table part 4 would allow the participants to present some of their results and express some domain of activities. Re4serach for collaboration will be identified.

Extended solvent-contact model approach to blind SAMPL5 prediction challenge for the distribution coefficients of drug-like molecules

NASA Astrophysics Data System (ADS)

Chung, Kee-Choo; Park, Hwangseo

2016-11-01

The performance of the extended solvent-contact model has been addressed in the SAMPL5 blind prediction challenge for distribution coefficient (LogD) of drug-like molecules with respect to the cyclohexane/water partitioning system. All the atomic parameters defined for 41 atom types in the solvation free energy function were optimized by operating a standard genetic algorithm with respect to water and cyclohexane solvents. In the parameterizations for cyclohexane, the experimental solvation free energy (Δ G sol ) data of 15 molecules for 1-octanol were combined with those of 77 molecules for cyclohexane to construct a training set because Δ G sol values of the former were unavailable for cyclohexane in publicly accessible databases. Using this hybrid training set, we established the LogD prediction model with the correlation coefficient ( R), average error (AE), and root mean square error (RMSE) of 0.55, 1.53, and 3.03, respectively, for the comparison of experimental and computational results for 53 SAMPL5 molecules. The modest accuracy in LogD prediction could be attributed to the incomplete optimization of atomic solvation parameters for cyclohexane. With respect to 31 SAMPL5 molecules containing the atom types for which experimental reference data for Δ G sol were available for both water and cyclohexane, the accuracy in LogD prediction increased remarkably with the R, AE, and RMSE values of 0.82, 0.89, and 1.60, respectively. This significant enhancement in performance stemmed from the better optimization of atomic solvation parameters by limiting the element of training set to the molecules with experimental Δ G sol data for cyclohexane. Due to the simplicity in model building and to low computational cost for parameterizations, the extended solvent-contact model is anticipated to serve as a valuable computational tool for LogD prediction upon the enrichment of experimental Δ G sol data for organic solvents.

Nanoarchitectonics of molecular aggregates: science and technology.

PubMed

Ramanathan, Muruganathan; Hong, Kunlun; Ji, Qingmin; Yonamine, Yusuke; Hill, Jonathan P; Ariga, Katsuhiko

2014-01-01

The field of making, studying and using molecular aggregates, in which the individual molecules (monomers) are arranged in a regular fashion, has come a long way. Taking control over the aggregation of small molecules and polymers in bulk, on surfaces and at interfaces pose a considerable challenge for their utilization in modern high tech applications. In this review, we provide a detailed insight into recent trends in molecular aggregates from the perspectives of nanoarchitectonics.

Nanoarchitectonics of Molecular Aggregates: Science and Technology

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

Ramanathan, Nathan Muruganathan; Hong, Kunlun; Ji, Dr. Qingmin

2014-01-01

The field of making, studying and using molecular aggregates, in which the individual molecules (monomers) are arranged in a regular fashion, has come a long way. Taking control over the aggregation of small molecules and polymers in bulk, on surfaces and at interfaces pose a considerable challenge for their utilization in modern high tech applications. In this review we provide a detailed insight into recent trends in molecular aggregates from the perspectives of nanoarchitectonics.

Intrinsic property measurement of surfactant-templated mesoporous silica films using time-resolved single-molecule imaging.

PubMed

Kennard, Raymond; DeSisto, William J; Giririjan, Thanu Praba; Mason, Michael D

2008-04-07

Mesoporous silica membranes fabricated by the surfactant-templated sol-gel process have received attention because of the potential to prepare membranes with a narrow pore size distribution and ordering of the interconnected pores. Potential applications include ultrafiltration, biological separations and drug delivery, and separators in lithium-ion batteries. Despite advancements in synthesis and characterization of these membranes, a quantitative description of the membrane microstructure remains a challenge. Currently the membrane microstructure is characterized by the combination of results from several techniques, i.e., gas permeance testing, x-ray diffraction scanning electron microscopy, transmission electron microscopy, and permporometry. The results from these ensemble methods are then compiled and the data fitted to a particular flow model. Although these methods are very effective in determining membrane performance, general pore size distribution, and defect concentration, they are unable to monitor molecular paths through the membrane and quantitatively measure molecular interactions between the molecular specie and pore network. Single-molecule imaging techniques enable optical measurements that probe materials on nanometer length scales through observation of individual molecules without the influence of averaging. Using single-molecule imaging spectroscopy, we can quantitatively characterize the interaction between the probe molecule and the interior of the pore within mesoporous silica membranes. This approach is radically different from typical membrane characterization methods in that it has the potential to spatially sample the underlying pore structure distribution, the surface energy, and the transport properties. Our hope is that this new fundamental knowledge can be quantitatively linked to both the preparation and the performance of membranes, leading to the advancement of membrane science and technology. Fluorescent molecules, 1,1-dioctadecyl-3,3,3,3-tetramethylindo-carbocyanine perchlorate, used to interrogate the available free volume in their vicinity, were loaded into the mesoporous silica membranes at subnanomolar concentrations. The mesoporous silica films were prepared using a nonionic ethylene oxide-propylene oxide-ethylene oxide triblock copolymer surfactant, Pluronic P123, on single crystal silicon substrates using dip coating of a silica sol. Membranes were prepared resulting in an average pore diameter of approximately 5 nm as measured by helium, nitrogen permeance, and porosimetry. Fluorescent images and time transient experiments were recorded using a custom built single-molecule scanning confocal microscope at differing temperatures (10, 20, 30, 40, and 50 degrees C). Time-dependent polarization anisotropy was used to obtain the enthalpy of adsorption and Henry's law constant of the probe molecule.

Intrinsic property measurement of surfactant-templated mesoporous silica films using time-resolved single-molecule imaging

NASA Astrophysics Data System (ADS)

Kennard, Raymond; DeSisto, William J.; Giririjan, Thanu Praba; Mason, Michael D.

2008-04-01

Mesoporous silica membranes fabricated by the surfactant-templated sol-gel process have received attention because of the potential to prepare membranes with a narrow pore size distribution and ordering of the interconnected pores. Potential applications include ultrafiltration, biological separations and drug delivery, and separators in lithium-ion batteries. Despite advancements in synthesis and characterization of these membranes, a quantitative description of the membrane microstructure remains a challenge. Currently the membrane microstructure is characterized by the combination of results from several techniques, i.e., gas permeance testing, x-ray diffraction scanning electron microscopy, transmission electron microscopy, and permporometry. The results from these ensemble methods are then compiled and the data fitted to a particular flow model. Although these methods are very effective in determining membrane performance, general pore size distribution, and defect concentration, they are unable to monitor molecular paths through the membrane and quantitatively measure molecular interactions between the molecular specie and pore network. Single-molecule imaging techniques enable optical measurements that probe materials on nanometer length scales through observation of individual molecules without the influence of averaging. Using single-molecule imaging spectroscopy, we can quantitatively characterize the interaction between the probe molecule and the interior of the pore within mesoporous silica membranes. This approach is radically different from typical membrane characterization methods in that it has the potential to spatially sample the underlying pore structure distribution, the surface energy, and the transport properties. Our hope is that this new fundamental knowledge can be quantitatively linked to both the preparation and the performance of membranes, leading to the advancement of membrane science and technology. Fluorescent molecules, 1,1-dioctadecyl-3,3,3,3-tetramethylindo-carbocyanine perchlorate, used to interrogate the available free volume in their vicinity, were loaded into the mesoporous silica membranes at subnanomolar concentrations. The mesoporous silica films were prepared using a nonionic ethylene oxide-propylene oxide-ethylene oxide triblock copolymer surfactant, Pluronic P123, on single crystal silicon substrates using dip coating of a silica sol. Membranes were prepared resulting in an average pore diameter of approximately 5nm as measured by helium, nitrogen permeance, and porosimetry. Fluorescent images and time transient experiments were recorded using a custom built single-molecule scanning confocal microscope at differing temperatures (10, 20, 30, 40, and 50°C). Time-dependent polarization anisotropy was used to obtain the enthalpy of adsorption and Henry's law constant of the probe molecule.

Identification of small molecules capable of regulating conformational changes of telomeric G-quadruplex

NASA Astrophysics Data System (ADS)

Chen, Shuo-Bin; Liu, Guo-Cai; Gu, Lian-Quan; Huang, Zhi-Shu; Tan, Jia-Heng

2018-02-01

Design of small molecules targeted at human telomeric G-quadruplex DNA is an extremely active research area. Interestingly, the telomeric G-quadruplex is a highly polymorphic structure. Changes in its conformation upon small molecule binding may be a powerful method to achieve a desired biological effect. However, the rational development of small molecules capable of regulating conformational change of telomeric G-quadruplex structures is still challenging. In this study, we developed a reliable ligand-based pharmacophore model based on isaindigotone derivatives with conformational change activity toward telomeric G-quadruplex DNA. Furthermore, virtual screening of database was conducted using this pharmacophore model and benzopyranopyrimidine derivatives in the database were identified as a strong inducer of the telomeric G-quadruplex DNA conformation, transforming it from hybrid-type structure to parallel structure.

Programmed self-assembly of large π-conjugated molecules into electroactive one-dimensional nanostructures

PubMed Central

Yamamoto, Yohei

2012-01-01

Electroactive one-dimensional (1D) nano-objects possess inherent unidirectional charge and energy transport capabilities along with anisotropic absorption and emission of light, which are of great advantage for the development of nanometer-scale electronics and optoelectronics. In particular, molecular nanowires formed by self-assembly of π-conjugated molecules attract increasing attention for application in supramolecular electronics. This review introduces recent topics related to electroactive molecular nanowires. The nanowires are classified into four categories with respect to the electronic states of the constituent molecules: electron donors, acceptors, donor–acceptor pairs and miscellaneous molecules that display interesting electronic properties. Although many challenges still remain for practical use, state-of-the-art 1D supramolecular nanomaterials have already brought significant advances to both fundamental chemical sciences and technological applications. PMID:27877488

Cellular Uptake of Tile-Assembled DNA Nanotubes.

PubMed

Kocabey, Samet; Meinl, Hanna; MacPherson, Iain S; Cassinelli, Valentina; Manetto, Antonio; Rothenfusser, Simon; Liedl, Tim; Lichtenegger, Felix S

2014-12-30

DNA-based nanostructures have received great attention as molecular vehicles for cellular delivery of biomolecules and cancer drugs. Here, we report on the cellular uptake of tubule-like DNA tile-assembled nanostructures 27 nm in length and 8 nm in diameter that carry siRNA molecules, folic acid and fluorescent dyes. In our observations, the DNA structures are delivered to the endosome and do not reach the cytosol of the GFP -expressing HeLa cells that were used in the experiments. Consistent with this observation, no elevated silencing of the GFP gene could be detected. Furthermore, the presence of up to six molecules of folic acid on the carrier surface did not alter the uptake behavior and gene silencing. We further observed several challenges that have to be considered when performing in vitro and in vivo experiments with DNA structures: (i) DNA tile tubes consisting of 42 nt-long oligonucleotides and carrying single- or double-stranded extensions degrade within one hour in cell medium at 37 °C, while the same tubes without extensions are stable for up to eight hours. The degradation is caused mainly by the low concentration of divalent ions in the media. The lifetime in cell medium can be increased drastically by employing DNA tiles that are 84 nt long. (ii) Dyes may get cleaved from the oligonucleotides and then accumulate inside the cell close to the mitochondria, which can lead to misinterpretation of data generated by flow cytometry and fluorescence microscopy. (iii) Single-stranded DNA carrying fluorescent dyes are internalized at similar levels as the DNA tile-assembled tubes used here.

Changes in brain cell shape create residual extracellular space volume and explain tortuosity behavior during osmotic challenge.

PubMed

Chen, K C; Nicholson, C

2000-07-18

Diffusion of molecules in brain extracellular space is constrained by two macroscopic parameters, tortuosity factor lambda and volume fraction alpha. Recent studies in brain slices show that when osmolarity is reduced, lambda increases while alpha decreases. In contrast, with increased osmolarity, alpha increases, but lambda attains a plateau. Using homogenization theory and a variety of lattice models, we found that the plateau behavior of lambda can be explained if the shape of brain cells changes nonuniformly during the shrinking or swelling induced by osmotic challenge. The nonuniform cellular shrinkage creates residual extracellular space that temporarily traps diffusing molecules, thus impeding the macroscopic diffusion. The paper also discusses the definition of tortuosity and its independence of the measurement frame of reference.

Degradation of Akt using protein-catalyzed capture agents.

PubMed

Henning, Ryan K; Varghese, Joseph O; Das, Samir; Nag, Arundhati; Tang, Grace; Tang, Kevin; Sutherland, Alexander M; Heath, James R

2016-04-01

Abnormal signaling of the protein kinase Akt has been shown to contribute to human diseases such as diabetes and cancer, but Akt has proven to be a challenging target for drugging. Using iterative in situ click chemistry, we recently developed multiple protein-catalyzed capture (PCC) agents that allosterically modulate Akt enzymatic activity in a protein-based assay. Here, we utilize similar PCCs to exploit endogenous protein degradation pathways. We use the modularity of the anti-Akt PCCs to prepare proteolysis targeting chimeric molecules that are shown to promote the rapid degradation of Akt in live cancer cells. These novel proteolysis targeting chimeric molecules demonstrate that the epitope targeting selectivity of PCCs can be coupled with non-traditional drugging moieties to inhibit challenging targets. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Chemical Biology Probes from Advanced DNA-encoded Libraries.

PubMed

Salamon, Hazem; Klika Škopić, Mateja; Jung, Kathrin; Bugain, Olivia; Brunschweiger, Andreas

2016-02-19

The identification of bioactive compounds is a crucial step toward development of probes for chemical biology studies. Screening of DNA-encoded small molecule libraries (DELs) has emerged as a validated technology to interrogate vast chemical space. DELs consist of chimeric molecules composed of a low-molecular weight compound that is conjugated to a DNA identifier tag. They are screened as pooled libraries using selection to identify "hits." Screening of DELs has identified numerous bioactive compounds. Some of these molecules were instrumental in gaining a deeper understanding of biological systems. One of the main challenges in the field is the development of synthesis methodology for DELs.

Intercomparison of stratospheric water vapor observed by satellite experiments - Stratospheric Aerosol and Gas Experiment II versus Limb Infrared Monitor of the Stratosphere and Atmospheric Trace Molecule Spectroscopy

NASA Technical Reports Server (NTRS)

Chiou, E. W.; Mccormick, M. P.; Mcmaster, L. R.; Chu, W. P.; Larsen, J. C.; Rind, D.; Oltmans, S.

1993-01-01

A comparison is made of the stratospheric water vapor measurements made by the satellite sensors of the Stratospheric Aerosol and Gas Experiment II (SAGE II), the Nimbus-7 LIMS, and the Spacelab 3 Atmospheric Trace Molecule Spectroscopy (ATMOS) experiment. It was found that, despite differences in the measurement techniques, sampling bias, and observational periods, the three experiments have disclosed a generally consistent pattern of stratospheric water vapor distribution. The only significant difference occurs at high southern altitudes in May below 18 km, where LIMS measurements were 2-3 ppmv greater than those of SAGE II and ATMOS.

On the uncertainty in single molecule fluorescent lifetime and energy emission measurements

NASA Technical Reports Server (NTRS)

Brown, Emery N.; Zhang, Zhenhua; Mccollom, Alex D.

1995-01-01

Time-correlated single photon counting has recently been combined with mode-locked picosecond pulsed excitation to measure the fluorescent lifetimes and energy emissions of single molecules in a flow stream. Maximum likelihood (ML) and least square methods agree and are optimal when the number of detected photons is large however, in single molecule fluorescence experiments the number of detected photons can be less than 20, 67% of those can be noise and the detection time is restricted to 10 nanoseconds. Under the assumption that the photon signal and background noise are two independent inhomogeneous poisson processes, we derive the exact joint arrival time probably density of the photons collected in a single counting experiment performed in the presence of background noise. The model obviates the need to bin experimental data for analysis, and makes it possible to analyze formally the effect of background noise on the photon detection experiment using both ML or Bayesian methods. For both methods we derive the joint and marginal probability densities of the fluorescent lifetime and fluorescent emission. the ML and Bayesian methods are compared in an analysis of simulated single molecule fluorescence experiments of Rhodamine 110 using different combinations of expected background nose and expected fluorescence emission. While both the ML or Bayesian procedures perform well for analyzing fluorescence emissions, the Bayesian methods provide more realistic measures of uncertainty in the fluorescent lifetimes. The Bayesian methods would be especially useful for measuring uncertainty in fluorescent lifetime estimates in current single molecule flow stream experiments where the expected fluorescence emission is low. Both the ML and Bayesian algorithms can be automated for applications in molecular biology.

On the Uncertainty in Single Molecule Fluorescent Lifetime and Energy Emission Measurements

NASA Technical Reports Server (NTRS)

Brown, Emery N.; Zhang, Zhenhua; McCollom, Alex D.

1996-01-01

Time-correlated single photon counting has recently been combined with mode-locked picosecond pulsed excitation to measure the fluorescent lifetimes and energy emissions of single molecules in a flow stream. Maximum likelihood (ML) and least squares methods agree and are optimal when the number of detected photons is large, however, in single molecule fluorescence experiments the number of detected photons can be less than 20, 67 percent of those can be noise, and the detection time is restricted to 10 nanoseconds. Under the assumption that the photon signal and background noise are two independent inhomogeneous Poisson processes, we derive the exact joint arrival time probability density of the photons collected in a single counting experiment performed in the presence of background noise. The model obviates the need to bin experimental data for analysis, and makes it possible to analyze formally the effect of background noise on the photon detection experiment using both ML or Bayesian methods. For both methods we derive the joint and marginal probability densities of the fluorescent lifetime and fluorescent emission. The ML and Bayesian methods are compared in an analysis of simulated single molecule fluorescence experiments of Rhodamine 110 using different combinations of expected background noise and expected fluorescence emission. While both the ML or Bayesian procedures perform well for analyzing fluorescence emissions, the Bayesian methods provide more realistic measures of uncertainty in the fluorescent lifetimes. The Bayesian methods would be especially useful for measuring uncertainty in fluorescent lifetime estimates in current single molecule flow stream experiments where the expected fluorescence emission is low. Both the ML and Bayesian algorithms can be automated for applications in molecular biology.

Using Multiorder Time-Correlation Functions (TCFs) To Elucidate Biomolecular Reaction Pathways from Microsecond Single-Molecule Fluorescence Experiments.

PubMed

Phelps, Carey; Israels, Brett; Marsh, Morgan C; von Hippel, Peter H; Marcus, Andrew H

2016-12-29

Recent advances in single-molecule fluorescence imaging have made it possible to perform measurements on microsecond time scales. Such experiments have the potential to reveal detailed information about the conformational changes in biological macromolecules, including the reaction pathways and dynamics of the rearrangements involved in processes, such as sequence-specific DNA "breathing" and the assembly of protein-nucleic acid complexes. Because microsecond-resolved single-molecule trajectories often involve "sparse" data, that is, they contain relatively few data points per unit time, they cannot be easily analyzed using the standard protocols that were developed for single-molecule experiments carried out with tens-of-millisecond time resolution and high "data density." Here, we describe a generalized approach, based on time-correlation functions, to obtain kinetic information from microsecond-resolved single-molecule fluorescence measurements. This approach can be used to identify short-lived intermediates that lie on reaction pathways connecting relatively long-lived reactant and product states. As a concrete illustration of the potential of this methodology for analyzing specific macromolecular systems, we accompany the theoretical presentation with the description of a specific biologically relevant example drawn from studies of reaction mechanisms of the assembly of the single-stranded DNA binding protein of the T4 bacteriophage replication complex onto a model DNA replication fork.

Elementary Reactions and Their Role in Gas-Phase Prebiotic Chemistry

PubMed Central

Balucani, Nadia

2009-01-01

The formation of complex organic molecules in a reactor filled with gaseous mixtures possibly reproducing the primitive terrestrial atmosphere and ocean demonstrated more than 50 years ago that inorganic synthesis of prebiotic molecules is possible, provided that some form of energy is provided to the system. After that groundbreaking experiment, gas-phase prebiotic molecules have been observed in a wide variety of extraterrestrial objects (including interstellar clouds, comets and planetary atmospheres) where the physical conditions vary widely. A thorough characterization of the chemical evolution of those objects relies on a multi-disciplinary approach: 1) observations allow us to identify the molecules and their number densities as they are nowadays; 2) the chemistry which lies behind their formation starting from atoms and simple molecules is accounted for by complex reaction networks; 3) for a realistic modeling of such networks, a number of experimental parameters are needed and, therefore, the relevant molecular processes should be fully characterized in laboratory experiments. A survey of the available literature reveals, however, that much information is still lacking if it is true that only a small percentage of the elementary reactions considered in the models have been characterized in laboratory experiments. New experimental approaches to characterize the relevant elementary reactions in laboratory are presented and the implications of the results are discussed. PMID:19564951

Rapid and accurate prediction and scoring of water molecules in protein binding sites.

PubMed

Ross, Gregory A; Morris, Garrett M; Biggin, Philip C

2012-01-01

Water plays a critical role in ligand-protein interactions. However, it is still challenging to predict accurately not only where water molecules prefer to bind, but also which of those water molecules might be displaceable. The latter is often seen as a route to optimizing affinity of potential drug candidates. Using a protocol we call WaterDock, we show that the freely available AutoDock Vina tool can be used to predict accurately the binding sites of water molecules. WaterDock was validated using data from X-ray crystallography, neutron diffraction and molecular dynamics simulations and correctly predicted 97% of the water molecules in the test set. In addition, we combined data-mining, heuristic and machine learning techniques to develop probabilistic water molecule classifiers. When applied to WaterDock predictions in the Astex Diverse Set of protein ligand complexes, we could identify whether a water molecule was conserved or displaced to an accuracy of 75%. A second model predicted whether water molecules were displaced by polar groups or by non-polar groups to an accuracy of 80%. These results should prove useful for anyone wishing to undertake rational design of new compounds where the displacement of water molecules is being considered as a route to improved affinity.

Proposed Molecular Beam Determination of Energy Partition in the Photodissociation of Polyatomic Molecules

DOE R&D Accomplishments Database

Zare, P. N.; Herschbach, D. R.

1964-01-29

Conventional photochemical experiments give no information about the partitioning of energy between translational recoil and internal excitation of the fragment molecules formed in photodissociation of a polyatomic molecule. In a molecular beam experiment, it becomes possible to determine the energy partition from the form of the laboratory angular distribution of one of the photodissociation products. A general kinematic analysis is worked out in detail, and the uncertainty introduced by the finite angular resolution of the apparatus and the velocity spread in the parent beam is examined. The experimental requirements are evaluated for he photolysis of methyl iodide by the 2537 angstrom Hg line.

DNA-cisplatin binding mechanism peculiarities studied with single molecule stretching experiments

NASA Astrophysics Data System (ADS)

Crisafuli, F. A. P.; Cesconetto, E. C.; Ramos, E. B.; Rocha, M. S.

2012-02-01

We propose a method to determine the DNA-cisplatin binding mechanism peculiarities by monitoring the mechanical properties of these complexes. To accomplish this task, we have performed single molecule stretching experiments by using optical tweezers, from which the persistence and contour lengths of the complexes can be promptly measured. The persistence length of the complexes as a function of the drug total concentration in the sample was used to deduce the binding data, from which we show that cisplatin binds cooperatively to the DNA molecule, a point which so far has not been stressed in binding equilibrium studies of this ligand.

Ligand cluster-based protein network and ePlatton, a multi-target ligand finder.

PubMed

Du, Yu; Shi, Tieliu

2016-01-01

Small molecules are information carriers that make cells aware of external changes and couple internal metabolic and signalling pathway systems with each other. In some specific physiological status, natural or artificial molecules are used to interact with selective biological targets to activate or inhibit their functions to achieve expected biological and physiological output. Millions of years of evolution have optimized biological processes and pathways and now the endocrine and immune system cannot work properly without some key small molecules. In the past thousands of years, the human race has managed to find many medicines against diseases by trail-and-error experience. In the recent decades, with the deepening understanding of life and the progress of molecular biology, researchers spare no effort to design molecules targeting one or two key enzymes and receptors related to corresponding diseases. But recent studies in pharmacogenomics have shown that polypharmacology may be necessary for the effects of drugs, which challenge the paradigm, 'one drug, one target, one disease'. Nowadays, cheminformatics and structural biology can help us reasonably take advantage of the polypharmacology to design next-generation promiscuous drugs and drug combination therapies. 234,591 protein-ligand interactions were extracted from ChEMBL. By the 2D structure similarity, 13,769 ligand emerged from 156,151 distinct ligands which were recognized by 1477 proteins. Ligand cluster- and sequence-based protein networks (LCBN, SBN) were constructed, compared and analysed. For assisting compound designing, exploring polypharmacology and finding possible drug combination, we integrated the pathway, disease, drug adverse reaction and the relationship of targets and ligand clusters into the web platform, ePlatton, which is available at http://www.megabionet.org/eplatton. Although there were some disagreements between the LCBN and SBN, communities in both networks were largely the same with normalized mutual information at 0.9. The study of target and ligand cluster promiscuity underlying the LCBN showed that light ligand clusters were more promiscuous than the heavy one and that highly connected nodes tended to be protein kinases and involved in phosphorylation. ePlatton considerably reduced the redundancy of the ligand set of targets and made it easy to deduce the possible relationship between compounds and targets, pathways and side effects. ePlatton behaved reliably in validation experiments and also fast in virtual screening and information retrieval.Graphical abstractCluster exemplars and ePlatton's mechanism.

Atomic and Molecular Systems in Intense Ultrashort Laser Pulses

NASA Astrophysics Data System (ADS)

Saenz, A.

2008-07-01

The full quantum mechanical treatment of atomic and molecular systems exposed to intense laser pulses is a so far unsolved challenge, even for systems as small as molecular hydrogen. Therefore, a number of simplified qualitative and quantitative models have been introduced in order to provide at least some interpretational tools for experimental data. The assessment of these models describing the molecular response is complicated, since a comparison to experiment requires often a number of averages to be performed. This includes in many cases averaging of different orientations of the molecule with respect to the laser field, focal volume effects, etc. Furthermore, the pulse shape and even the peak intensity is experimentally not known with very high precision; considering, e.g., the exponential intensity dependence of the ionization signal. Finally, experiments usually provide only relative yields. As a consequence of all these averagings and uncertainties, it is possible that different models may successfully explain some experimental results or features, although these models disagree substantially, if their predictions are compared before averaging. Therefore, fully quantum-mechanical approaches at least for small atomic and molecular systems are highly desirable and have been developed in our group. This includes efficient codes for solving the time-dependent Schrodinger equation of atomic hydrogen, helium or other effective one- or two-electron atoms as well as for the electronic motion in linear (effective) one-and two-electron diatomic molecules like H_2.Very recently, a code for larger molecular systems that adopts the so-called single-active electron approximation was also successfully implemented and applied. In the first part of this talk popular models describing intense laser-field ionization of atoms and their extensions to molecules are described. Then their validity is discussed on the basis of quantum-mechanical calculations. Finally, some peculiar molecular strong-field effects and the possibility of strong-field control mechanisms will be demonstrated. This includes phenomena like enhanced ionization and bond softening as well as the creation of vibrational wavepacket in the non-ionized electronic ground state of H_2 by creating a Schrodinger-cat state between the ionized and the non-ionized molecules. The latter, theoretically predicted phenomenon was very recently experimentally observed and lead to the real-time observation of the so far fastest molecular motion.

Accuracy of theory for calculating electron impact ionization of molecules

NASA Astrophysics Data System (ADS)

Chaluvadi, Hari Hara Kumar

The study of electron impact single ionization of atoms and molecules has provided valuable information about fundamental collisions. The most detailed information is obtained from triple differential cross sections (TDCS) in which the energy and momentum of all three final state particles are determined. These cross sections are much more difficult for theory since the detailed kinematics of the experiment become important. There are many theoretical approximations for ionization of molecules. One of the successful methods is the molecular 3-body distorted wave (M3DW) approximation. One of the strengths of the DW approximation is that it can be applied for any energy and any size molecule. One of the approximations that has been made to significantly reduce the required computer time is the OAMO (orientation averaged molecular orbital) approximation. In this dissertation, the accuracy of the M3DW-OAMO is tested for different molecules. Surprisingly, the M3DW-OAMO approximation yields reasonably good agreement with experiment for ionization of H2 and N2. On the other hand, the M3DW-OAMO results for ionization of CH4, NH3 and DNA derivative molecules did not agree very well with experiment. Consequently, we proposed the M3DW with a proper average (PA) calculation. In this dissertation, it is shown that the M3DW-PA calculations for CH4 and SF6 are in much better agreement with experimental data than the M3DW-OAMO results.

Fast experiments for structure elucidation of small molecules: Hadamard NMR with multiple receivers.

PubMed

Gierth, Peter; Codina, Anna; Schumann, Frank; Kovacs, Helena; Kupče, Ēriks

2015-11-01

We propose several significant improvements to the PANSY (Parallel NMR SpectroscopY) experiments-PANSY COSY and PANSY-TOCSY. The improved versions of these experiments provide sufficient spectral information for structure elucidation of small organic molecules from just two 2D experiments. The PANSY-TOCSY-Q experiment has been modified to allow for simultaneous acquisition of three different types of NMR spectra-1D C-13 of non-protonated carbon sites, 2D TOCSY and multiplicity edited 2D HETCOR. In addition the J-filtered 2D PANSY-gCOSY experiment records a 2D HH gCOSY spectrum in parallel with a (1) J-filtered HC long-range HETCOR spectrum as well as offers a simplified data processing. In addition to parallel acquisition, further time savings are feasible because of significantly smaller F1 spectral windows as compared to the indirect detection experiments. Use of cryoprobes and multiple receivers can significantly alleviate the sensitivity issues that are usually associated with the so called direct detection experiments. In cases where experiments are sampling limited rather than sensitivity limited further reduction of experiment time is achieved by using Hadamard encoding. In favorable cases the total recording time for the two PANSY experiments can be reduced to just 40 s. The proposed PANSY experiments provide sufficient information to allow the CMCse software package (Bruker) to solve structures of small organic molecules. Copyright © 2015 John Wiley & Sons, Ltd.

Identification of vibrational signatures from short chains of interlinked molecule-nanoparticle junctions obtained by inelastic electron tunnelling spectroscopy

NASA Astrophysics Data System (ADS)

Jafri, S. H. M.; Löfås, H.; Fransson, J.; Blom, T.; Grigoriev, A.; Wallner, A.; Ahuja, R.; Ottosson, H.; Leifer, K.

2013-05-01

Short chains containing a series of metal-molecule-nanoparticle nanojunctions are a nano-material system with the potential to give electrical signatures close to those from single molecule experiments while enabling us to build portable devices on a chip. Inelastic electron tunnelling spectroscopy (IETS) measurements provide one of the most characteristic electrical signals of single and few molecules. In interlinked molecule-nanoparticle (NP) chains containing typically 5-7 molecules in a chain, the spectrum is expected to be a superposition of the vibrational signatures of individual molecules. We have established a stable and reproducible molecule-AuNP multi-junction by placing a few 1,8-octanedithiol (ODT) molecules onto a versatile and portable nanoparticle-nanoelectrode platform and measured for the first time vibrational molecular signatures at complex and coupled few-molecule-NP junctions. From quantum transport calculations, we model the IETS spectra and identify vibrational modes as well as the number of molecules contributing to the electron transport in the measured spectra.Short chains containing a series of metal-molecule-nanoparticle nanojunctions are a nano-material system with the potential to give electrical signatures close to those from single molecule experiments while enabling us to build portable devices on a chip. Inelastic electron tunnelling spectroscopy (IETS) measurements provide one of the most characteristic electrical signals of single and few molecules. In interlinked molecule-nanoparticle (NP) chains containing typically 5-7 molecules in a chain, the spectrum is expected to be a superposition of the vibrational signatures of individual molecules. We have established a stable and reproducible molecule-AuNP multi-junction by placing a few 1,8-octanedithiol (ODT) molecules onto a versatile and portable nanoparticle-nanoelectrode platform and measured for the first time vibrational molecular signatures at complex and coupled few-molecule-NP junctions. From quantum transport calculations, we model the IETS spectra and identify vibrational modes as well as the number of molecules contributing to the electron transport in the measured spectra. Electronic supplementary information (ESI) available: Methods and materials. Details of the ab initio calculation of molecular vibrations and inelastic spectra of ODT between two Au electrodes. A model of carrier transport through the molecular junctions. See DOI: 10.1039/c3nr00505d

Micromanipulation by laser microbeam and optical tweezers: from plant cells to single molecules.

PubMed

Greulich, K O; Pilarczyk, G; Hoffmann, A; Meyer Zu Hörste, G; Schäfer, B; Uhl, V; Monajembashi, S

2000-06-01

Complete manipulation by laser light allows precise and gentle treatment of plant cells, subcellular structures, and even individual DNA molecules. Recently, affordable lasers have become available for the construction of microbeams as well as for optical tweezers. This may generate new interest in these tools for plant biologists. Early experiments, reviewed in this journal, showed that laser supported microinjection of material into plant cells or tissues circumvents mechanical problems encountered in microinjection by fragile glass capillaries. Plant protoplasts could be fused with each other when under microscopical observation, and it was no major problem to generate a triple or quadruple fusion product. In the present paper we review experiments where membrane material was prepared from root hair tips and microgravity was simulated in algae. As many plant cells are transparent, it is possible to work inside living, intact cells. New experiments show that it is possible to release by optical micromanipulation, with high spatial resolutions, intracellular calcium from caged compounds and to study calcium oscillations. An example for avian cardiac tissue is given, but the technique is also suitable for plant cell research. As a more technical tool, optical tweezers can be used to spatially fix subcellular structures otherwise moving inside a cell and thus make them available for investigation with a confocal microscope even when the time for image formation is extended (for example at low fluorescence emission). A molecular biological example is the handling of chromosomes and isolated individual DNA molecules by laser microtools. For example, chromosomes can be cut along complex trajectories, not only perpendicular to their long axis. Single DNA molecules are cut by the laser microbeam and, after coupling such a molecule to a polystrene microbead, are handled in complex geometries. Here, the individual DNA molecules are made visible with a conventional fluorescence microscope by fluorescent dyes such as SYBRGreen. The cutting of a single DNA molecule by molecules of the restriction endonuclease EcoRI can be observed directly, i.e. a type of single molecule restriction analysis is possible. Finally, mechanical properties of individual DNA molecules can be observed directly.

Participation of CD11b and F4/80 molecules in the conjunctival eosinophilia of experimental allergic conjunctivitis.

PubMed

Fukushima, Atsuki; Ishida, Waka; Ojima, Ayako; Kajisako, Mina; Sumi, Tamaki; Yamada, Jun; Tsuru, Emi; Miyazaki, Jun-ichi; Tominaga, Akira; Yagita, Hideo

2010-01-01

CD11b and F4/80 are macrophage surface markers. How these molecules participate in allergic eosinophil infiltration remains unclear. We examined the roles CD11b and F4/80 play in the conjunctival eosinophil infiltration associated with experimental allergic conjunctivitis. Ragweed-immunized BALB/c mice were challenged with ragweed in eye drops to induce conjunctival eosinophil infiltration. The effect of challenge on conjunctival CD11b+ and F4/80+ cell numbers was determined by immunohistochemistry. In the same model, blocking anti-CD11b and anti-F4/80 Abs were injected intraperitoneally during the induction or the effector phase, or subconjunctivally 2 h before challenge, to determine their effect on challenge-induced conjunctival eosinophilia. To examine whether eosinophils express CD11b and F4/80 molecules, splenocytes from IL-5 gene-electroporated mice were subjected to flow cytometric analysis. To clarify the involvement of CD11b and F4/80 in conjunctival eosinophil infiltration, mice were intraperitoneally injected with anti-CD11b and anti-F4/80 Abs and then subconjunctivally injected with eotaxin to induce conjunctival eosinophilia. Ragweed challenge elevated conjunctival CD11b+ and F4/80+ cell numbers. Systemic anti-CD11b and anti-F4/80 Ab treatments during the effector phase, but not in either the induction phase or the local injection of Ab, suppressed conjunctival eosinophil infiltration in ragweed-induced conjunctivitis. Most splenic eosinophils from IL-5 gene-introduced mice expressed CD11b and F4/80. Systemic anti-CD11b and anti-F4/80 Ab treatment suppressed conjunctival eosinophilia induced by subconjunctival eotaxin injection. CD11b and F4/80 appear to participate in conjunctival eosinophil infiltration in allergic conjunctivitis. Their involvement in conjunctival eosinophilia appears to be due to their expression on eosinophils rather than on macrophages. 2009 S. Karger AG, Basel.

Activated leucocyte cell adhesion molecule (ALCAM/CD166) regulates T cell responses in a murine model of food allergy.

PubMed

Kim, Y S; Kim, M N; Lee, K E; Hong, J Y; Oh, M S; Kim, S Y; Kim, K W; Sohn, M H

2018-05-01

Food allergy is a major public health problem. Studies have shown that long-term interactions between activated leucocyte cell adhesion molecule (ALCAM/CD166) on the surface of antigen-presenting cells, and CD6, a co-stimulatory molecule, influence immune responses. However, there are currently no studies on the functions of ALCAM in food allergy. Therefore, we aimed to identify the functions of ALCAM in ovalbumin (OVA)-induced food allergy using ALCAM-deficient mice. Wild-type (WT) and ALCAM-deficient (ALCAM -/- ) mice were sensitized intraperitoneally and with orally fed OVA. The mice were killed, and parameters related to food allergy and T helper type 2 (Th2) immune responses were analysed. ALCAM serum levels increased and mRNA expression decreased in OVA-challenged WT mice. Serum immunoglobulin (Ig)E levels, Th2 cytokine mRNA and histological injuries were higher in OVA-challenged WT mice than in control mice, and these were attenuated in ALCAM -/- mice. T cell proliferation of total cells, CD3 + CD4 + T cells and activated T cells in immune tissues were diminished in OVA-challenged ALCAM -/- mice. Proliferation of co-cultured T cells and dendritic cells (DCs) was decreased by the anti-CD6 antibody. In addition, WT mice sensitized by adoptive transfer of OVA-pulsed ALCAM -/- BM-derived DCs showed reduced immune responses. Lastly, serum ALCAM levels were higher in children with food allergy than in control subjects. In this study, serum levels of ALCAM were elevated in food allergy-induced WT mice and children with food allergy. Moreover, immune responses and T cell activation were attenuated in OVA-challenged ALCAM -/- mice. These results indicate that ALCAM regulates food allergy by affecting T cell activation. © 2018 British Society for Immunology.

Applying Tandem Mass Spectral Libraries for Solving the Critical Assessment of Small Molecule Identification (CASMI) LC/MS Challenge 2012

PubMed Central

Oberacher, Herbert

2013-01-01

The “Critical Assessment of Small Molecule Identification” (CASMI) contest was aimed in testing strategies for small molecule identification that are currently available in the experimental and computational mass spectrometry community. We have applied tandem mass spectral library search to solve Category 2 of the CASMI Challenge 2012 (best identification for high resolution LC/MS data). More than 230,000 tandem mass spectra part of four well established libraries (MassBank, the collection of tandem mass spectra of the “NIST/NIH/EPA Mass Spectral Library 2012”, METLIN, and the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’) were searched. The sample spectra acquired in positive ion mode were processed. Seven out of 12 challenges did not produce putative positive matches, simply because reference spectra were not available for the compounds searched. This suggests that to some extent the limited coverage of chemical space with high-quality reference spectra is still a problem encountered in tandem mass spectral library search. Solutions were submitted for five challenges. Three compounds were correctly identified (kanamycin A, benzyldiphenylphosphine oxide, and 1-isopropyl-5-methyl-1H-indole-2,3-dione). In the absence of any reference spectrum, a false positive identification was obtained for 1-aminoanthraquinone by matching the corresponding sample spectrum to the structurally related compounds N-phenylphthalimide and 2-aminoanthraquinone. Another false positive result was submitted for 1H-benz[g]indole; for the 1H-benz[g]indole-specific sample spectra provided, carbazole was listed as the best matching compound. In this case, the quality of the available 1H-benz[g]indole-specific reference spectra was found to hamper unequivocal identification. PMID:24957994

Investigation of the RbCa molecule: Experiment and theory.

PubMed

Pototschnig, Johann V; Krois, Günter; Lackner, Florian; Ernst, Wolfgang E

2015-04-01

We present a thorough theoretical and experimental study of the electronic structure of RbCa. The mixed alkali-alkaline earth molecule RbCa was formed on superfluid helium nanodroplets. Excited states of the molecule in the range of 13 000-23 000 cm -1 were recorded by resonance enhanced multi-photon ionization time-of-flight spectroscopy. The experiment is accompanied by high level ab initio calculations of ground and excited state properties, utilizing a multireference configuration interaction method based on multiconfigurational self consistent field calculations. With this approach the potential energy curves and permanent electric dipole moments of 24 electronic states were calculated. In addition we computed the transition dipole moments for transitions from the ground into excited states. The combination of experiment and theory allowed the assignment of features in the recorded spectrum to the excited [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text] states, where the experiment allowed to benchmark the calculation. This is the first experimental work giving insight into the previously unknown RbCa molecule, which offers great prospects in ultracold molecular physics due to its magnetic and electronic dipole moment in the [Formula: see text] ground state.

Measurement of the velocity of neutral fragments by the "correlated ion and neutral time of flight" method combined with "velocity-map imaging"

NASA Astrophysics Data System (ADS)

Berthias, F.; Feketeová, L.; Della Negra, R.; Dupasquier, T.; Fillol, R.; Abdoul-Carime, H.; Farizon, B.; Farizon, M.; Märk, T. D.

2017-08-01

In the challenging field of imaging molecular dynamics, a novel method has been developed and implemented that allows the measurement of the velocity of neutral fragments produced in collision induced dissociation experiments on an event-by-event basis. This has been made possible by combining a correlated ion and neutral time of flight method with a velocity map imaging technique. This new method relies on a multiparametric correlated detection of the neutral and charged fragments from collision induced dissociation on one single detector. Its implementation on the DIAM device (Device for irradiation of biomolecular clusters) (Dispositif d'Irradiation d'Agrégats bioMoléculaires) allowed us to measure the velocity distribution of water molecules evaporated from collision induced dissociation of mass- and energy-selected protonated water clusters.

Adsorption of organic ligands on low surface charge clay minerals: the composition in the aqueous interface region.

PubMed

Jelavić, S; Stipp, S L S; Bovet, N

2018-06-27

An understanding of the mechanisms that control the adsorption of organic molecules on clay minerals is of interest in several branches of science and industry. Oil production using low salinity injection fluids can increase yields by as much as 40% over standard injection with seawater or formation water. The mechanism responsible for the low salinity response is still debated, but one hypothesis is a change in pore surface wettability. Organic contamination in soil and drinking water aquifers is a challenge for municipal water suppliers and for agriculture. A better understanding is needed for how mineral species, solution composition and pH affect the desorption of low molecular weight organic ligands from clay minerals and consequently their wettability. We used X-ray photoelectron spectroscopy under cryogenic conditions to investigate the in situ composition in the mineral-solution interface region in a series of experiments with a range of pH and ion concentrations. We demonstrate that both chlorite and kaolinite release organic molecules under conditions relevant for low salinity water flooding. This release increases with a higher solution pH but is only slightly affected by the character of the organic ligand. This is consistent with the observation that low salinity enhanced oil recovery correlates with the presence of chlorite and kaolinite. Our results indicate that the pore surface charge and salinity of formation water and injection fluids are key parameters in determining the low salinity response. In general, our results imply that clay mineral surface charge influences the composition in the interface through an affinity for organic molecules.

Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38α MAP kinase: a combined computational and experimental study.

PubMed

Zhu, Shun; Travis, Sue M; Elcock, Adrian H

2013-07-09

A major current challenge for drug design efforts focused on protein kinases is the development of drug resistance caused by spontaneous mutations in the kinase catalytic domain. The ubiquity of this problem means that it would be advantageous to develop fast, effective computational methods that could be used to determine the effects of potential resistance-causing mutations before they arise in a clinical setting. With this long-term goal in mind, we have conducted a combined experimental and computational study of the thermodynamic effects of active-site mutations on a well-characterized and high-affinity interaction between a protein kinase and a small-molecule inhibitor. Specifically, we developed a fluorescence-based assay to measure the binding free energy of the small-molecule inhibitor, SB203580, to the p38α MAP kinase and used it measure the inhibitor's affinity for five different kinase mutants involving two residues (Val38 and Ala51) that contact the inhibitor in the crystal structure of the inhibitor-kinase complex. We then conducted long, explicit-solvent thermodynamic integration (TI) simulations in an attempt to reproduce the experimental relative binding affinities of the inhibitor for the five mutants; in total, a combined simulation time of 18.5 μs was obtained. Two widely used force fields - OPLS-AA/L and Amber ff99SB-ILDN - were tested in the TI simulations. Both force fields produced excellent agreement with experiment for three of the five mutants; simulations performed with the OPLS-AA/L force field, however, produced qualitatively incorrect results for the constructs that contained an A51V mutation. Interestingly, the discrepancies with the OPLS-AA/L force field could be rectified by the imposition of position restraints on the atoms of the protein backbone and the inhibitor without destroying the agreement for other mutations; the ability to reproduce experiment depended, however, upon the strength of the restraints' force constant. Imposition of position restraints in corresponding simulations that used the Amber ff99SB-ILDN force field had little effect on their ability to match experiment. Overall, the study shows that both force fields can work well for predicting the effects of active-site mutations on small molecule binding affinities and demonstrates how a direct combination of experiment and computation can be a powerful strategy for developing an understanding of protein-inhibitor interactions.

Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2

NASA Astrophysics Data System (ADS)

Kadukova, Maria; Grudinin, Sergei

2018-01-01

The 2016 D3R Grand Challenge 2 provided an opportunity to test multiple protein-ligand docking protocols on a set of ligands bound to farnesoid X receptor that has many available experimental structures. We participated in the Stage 1 of the Challenge devoted to the docking pose predictions, with the mean RMSD value of our submission poses of 2.9 Å. Here we present a thorough analysis of our docking predictions made with AutoDock Vina and the Convex-PL rescoring potential by reproducing our submission protocol and running a series of additional molecular docking experiments. We conclude that a correct receptor structure, or more precisely, the structure of the binding pocket, plays the crucial role in the success of our docking studies. We have also noticed the important role of a local ligand geometry, which seems to be not well discussed in literature. We succeed to improve our results up to the mean RMSD value of 2.15-2.33 Å dependent on the models of the ligands, if docking these to all available homologous receptors. Overall, for docking of ligands of diverse chemical series we suggest to perform docking of each of the ligands to a set of multiple receptors that are homologous to the target.

Cooperative CO2 Absorption Isotherms from a Bifunctional Guanidine and Bifunctional Alcohol.

PubMed

Steinhardt, Rachel; Hiew, Stanley C; Mohapatra, Hemakesh; Nguyen, Du; Oh, Zachary; Truong, Richard; Esser-Kahn, Aaron

2017-12-27

Designing new liquids for CO 2 absorption is a challenge in CO 2 removal. Here, achieving low regeneration energies while keeping high selectivity and large capacity are current challenges. Recent cooperative metal-organic frameworks have shown the potential to address many of these challenges. However, many absorbent systems and designs rely on liquid capture agents. We present herein a liquid absorption system which exhibits cooperative CO 2 absorption isotherms. Upon introduction, CO 2 uptake is initially suppressed, followed by an abrupt increase in absorption. The liquid consists of a bifunctional guanidine and bifunctional alcohol, which, when dissolved in bis(2-methoxyethyl) ether, forms a secondary viscous phase within seconds in response to increases in CO 2 . The precipitation of this second viscous phase drives CO 2 absorption from the gas phase. The isotherm of the bifunctional system differs starkly from the analogous monofunctional system, which exhibits limited CO 2 uptake across the same pressure range. In our system, CO 2 absorption is strongly solvent dependent. In DMSO, both systems exhibit hyperbolic isotherms and no precipitation occurs. Subsequent 1 H NMR experiments confirmed the formation of distinct alkylcarbonate species having either one or two molecules of CO 2 bound. The solvent and structure relationships derived from these results can be used to tailor new liquid absorption systems to the conditions of a given CO 2 separation process.

Neuronal Responses to Physiological Stress

PubMed Central

Kagias, Konstantinos; Nehammer, Camilla; Pocock, Roger

2012-01-01

Physiological stress can be defined as any external or internal condition that challenges the homeostasis of a cell or an organism. It can be divided into three different aspects: environmental stress, intrinsic developmental stress, and aging. Throughout life all living organisms are challenged by changes in the environment. Fluctuations in oxygen levels, temperature, and redox state for example, trigger molecular events that enable an organism to adapt, survive, and reproduce. In addition to external stressors, organisms experience stress associated with morphogenesis and changes in inner chemistry during normal development. For example, conditions such as intrinsic hypoxia and oxidative stress, due to an increase in tissue mass, have to be confronted by developing embryos in order to complete their development. Finally, organisms face the challenge of stochastic accumulation of molecular damage during aging that results in decline and eventual death. Studies have shown that the nervous system plays a pivotal role in responding to stress. Neurons not only receive and process information from the environment but also actively respond to various stresses to promote survival. These responses include changes in the expression of molecules such as transcription factors and microRNAs that regulate stress resistance and adaptation. Moreover, both intrinsic and extrinsic stresses have a tremendous impact on neuronal development and maintenance with implications in many diseases. Here, we review the responses of neurons to various physiological stressors at the molecular and cellular level. PMID:23112806

Identification of New Antifungal Compounds Targeting Thioredoxin Reductase of Paracoccidioides Genus

PubMed Central

Abadio, Ana Karina Rodrigues; Kioshima, Erika Seki; Leroux, Vincent; Martins, Natalia Florêncio; Maigret, Bernard; Felipe, Maria Sueli Soares

2015-01-01

The prevalence of invasive fungal infections worldwide has increased in the last decades. The development of specific drugs targeting pathogenic fungi without producing collateral damage to mammalian cells is a daunting pharmacological challenge. Indeed, many of the toxicities and drug interactions observed with contemporary antifungal therapies can be attributed to “nonselective” interactions with enzymes or cell membrane systems found in mammalian host cells. A computer-aided screening strategy against the TRR1 protein of Paracoccidioides lutzii is presented here. Initially, a bank of commercially available compounds from Life Chemicals provider was docked to model by virtual screening simulations. The small molecules that interact with the model were ranked and, among the best hits, twelve compounds out of 3,000 commercially-available candidates were selected. These molecules were synthesized for validation and in vitro antifungal activity assays for Paracoccidioides lutzii and P. brasiliensis were performed. From 12 molecules tested, 3 harbor inhibitory activity in antifungal assays against the two pathogenic fungi. Corroborating these findings, the molecules have inhibitory activity against the purified recombinant enzyme TRR1 in biochemical assays. Therefore, a rational combination of molecular modeling simulations and virtual screening of new drugs has provided a cost-effective solution to an early-stage medicinal challenge. These results provide a promising technique to the development of new and innovative drugs. PMID:26569405

Accurate prediction of personalized olfactory perception from large-scale chemoinformatic features.

PubMed

Li, Hongyang; Panwar, Bharat; Omenn, Gilbert S; Guan, Yuanfang

2018-02-01

The olfactory stimulus-percept problem has been studied for more than a century, yet it is still hard to precisely predict the odor given the large-scale chemoinformatic features of an odorant molecule. A major challenge is that the perceived qualities vary greatly among individuals due to different genetic and cultural backgrounds. Moreover, the combinatorial interactions between multiple odorant receptors and diverse molecules significantly complicate the olfaction prediction. Many attempts have been made to establish structure-odor relationships for intensity and pleasantness, but no models are available to predict the personalized multi-odor attributes of molecules. In this study, we describe our winning algorithm for predicting individual and population perceptual responses to various odorants in the DREAM Olfaction Prediction Challenge. We find that random forest model consisting of multiple decision trees is well suited to this prediction problem, given the large feature spaces and high variability of perceptual ratings among individuals. Integrating both population and individual perceptions into our model effectively reduces the influence of noise and outliers. By analyzing the importance of each chemical feature, we find that a small set of low- and nondegenerative features is sufficient for accurate prediction. Our random forest model successfully predicts personalized odor attributes of structurally diverse molecules. This model together with the top discriminative features has the potential to extend our understanding of olfactory perception mechanisms and provide an alternative for rational odorant design.

Dynamic fluctuations in single-molecule biophysics experiments. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

NASA Astrophysics Data System (ADS)

Krapf, Diego

2015-06-01

Single-molecule biophysics includes the study of isolated molecules and that of individual molecules within living cells. In both cases, dynamic fluctuations at the nanoscale play a critical role. Colomb and Sarkar emphasize how different noise sources affect the analysis of single molecule data [1]. Fluctuations in biomolecular systems arise from two very different mechanisms. On one hand thermal fluctuations are a predominant feature in the behavior of individual molecules. On the other hand, non-Gaussian fluctuations can arise from inter- and intramolecular interactions [2], spatial heterogeneities [3], non-Poisson external perturbations [4] and complex non-linear dynamics in general [5,6].

Synthesis of {111} Facet-Exposed MgO with Surface Oxygen Vacancies for Reactive Oxygen Species Generation in the Dark.

PubMed

Hao, Ying-Juan; Liu, Bing; Tian, Li-Gang; Li, Fa-Tang; Ren, Jie; Liu, Shao-Jia; Liu, Ying; Zhao, Jun; Wang, Xiao-Jing

2017-04-12

Seeking a simple and moderate route to generate reactive oxygen species (ROS) for antibiosis is of great interest and challenge. This work demonstrates that molecule transition and electron rearrangement processes can directly occur only through chemisorption interaction between the adsorbed O 2 and high-energy {111} facet-exposed MgO with abundant surface oxygen vacancies (SOVs), hence producing singlet oxygen and superoxide anion radicals without light irradiation. These ROS were confirmed by electron paramagnetic resonance, in situ Raman, and scavenger experiments. Furthermore, heat plays a crucial role for the electron transfer process to accelerate the formation of ·O 2 - , which is verified by temperature kinetic experiments of nitro blue tetrazolium reduction in the dark. Therefore, the presence of oxygen vacancy can be considered as an intensification of the activation process. The designed MgO is acquired in one step via constructing a reduction atmosphere during the combustion reaction process, which has an ability similar to that of noble metal Pd to activate molecular oxygen and can be used as an effective bacteriocide in the dark.

Modulating peroxisome proliferator–activated receptors for therapeutic benefit? Biology, clinical experience, and future prospects

PubMed Central

Rosenson, Robert S.; Wright, R. Scott; Farkouh, Michael; Plutzky, Jorge

2014-01-01

Clinical trials of cardiovascular disease (CVD) prevention in patients with type 2 diabetes mellitus primarily have been directed at the modification of a single major risk factor; however, in trials that enroll patients with and without diabetes, the absolute risk in CVD events remains higher in patients with diabetes. Efforts to reduce the macrovascular and microvascular residual risk have been directed toward a multifactorial CVD risk-factor modification; nonetheless, long-term complications remain high. Dual-peroxisome proliferator–activated receptor (PPAR) α/γ agonists may offer opportunities to lower macrovascular and microvascular complications of type 2 diabetes mellitus beyond the reductions achieved with conventional risk-factor modification. The information presented elucidates the differentiation of compound-specific vs class-effect properties of PPARs as the basis for future development of a new candidate molecule. Prior experience with thiazolidinediones, an approved class of PPARγ agonists, and glitazars, investigational class of dual-PPARα/γ agonists, also provides important lessons about the risks and benefits of targeting a nuclear receptor while revealing some of the future challenges for regulatory approval. PMID:23137497

The SAMPL4 host-guest blind prediction challenge: an overview.

PubMed

Muddana, Hari S; Fenley, Andrew T; Mobley, David L; Gilson, Michael K

2014-04-01

Prospective validation of methods for computing binding affinities can help assess their predictive power and thus set reasonable expectations for their performance in drug design applications. Supramolecular host-guest systems are excellent model systems for testing such affinity prediction methods, because their small size and limited conformational flexibility, relative to proteins, allows higher throughput and better numerical convergence. The SAMPL4 prediction challenge therefore included a series of host-guest systems, based on two hosts, cucurbit[7]uril and octa-acid. Binding affinities in aqueous solution were measured experimentally for a total of 23 guest molecules. Participants submitted 35 sets of computational predictions for these host-guest systems, based on methods ranging from simple docking, to extensive free energy simulations, to quantum mechanical calculations. Over half of the predictions provided better correlations with experiment than two simple null models, but most methods underperformed the null models in terms of root mean squared error and linear regression slope. Interestingly, the overall performance across all SAMPL4 submissions was similar to that for the prior SAMPL3 host-guest challenge, although the experimentalists took steps to simplify the current challenge. While some methods performed fairly consistently across both hosts, no single approach emerged as consistent top performer, and the nonsystematic nature of the various submissions made it impossible to draw definitive conclusions regarding the best choices of energy models or sampling algorithms. Salt effects emerged as an issue in the calculation of absolute binding affinities of cucurbit[7]uril-guest systems, but were not expected to affect the relative affinities significantly. Useful directions for future rounds of the challenge might involve encouraging participants to carry out some calculations that replicate each others' studies, and to systematically explore parameter options.

Improved transparency--nonlinearity trade-off with boroxine-based octupolar molecules.

PubMed

Alcaraz, Gilles; Euzenat, Lisenn; Mongin, Olivier; Katan, Claudine; Ledoux, Isabelle; Zyss, Joseph; Blanchard-Desce, Mireille; Vaultier, Michel

2003-11-21

A series of octupolar molecules derived from the boroxine framework were designed and their optical nonlinearities were investigated by performing harmonic light scattering experiments in solution; the molecules were found to combine excellent transparency in the near UV-visible region (lambdamax < or = 280 nm) and significant first-order hyperpolarisabilities (up to beta(0) = 56 x 10(-30) esu).

Hyperfine structure of 2Σ molecules containing alkaline-earth-metal atoms

NASA Astrophysics Data System (ADS)

Aldegunde, Jesus; Hutson, Jeremy M.

2018-04-01

Ultracold molecules with both electron spin and an electric dipole moment offer new possibilities in quantum science. We use density-functional theory to calculate hyperfine coupling constants for a selection of molecules important in this area, including RbSr, LiYb, RbYb, CaF, and SrF. We find substantial hyperfine coupling constants for the fermionic isotopes of the alkaline-earth-metal and Yb atoms. We discuss the hyperfine level patterns and Zeeman splittings expected for these molecules. The results will be important both to experiments aimed at forming ultracold open-shell molecules and to their applications.

Introduction to the Minireview Series on Modern Technologies for In-cell Biochemistry.

PubMed

Lutsenko, Svetlana

2016-02-19

The last decade has seen enormous progress in the exploration and understanding of the behavior of molecules in their natural cellular environments at increasingly high spatial and temporal resolution. Advances in microscopy and the development of new fluorescent reagents as well as genetic editing techniques have enabled quantitative analysis of protein interactions, intracellular trafficking, metabolic changes, and signaling. Modern biochemistry now faces new and exciting challenges. Can traditionally "in vitro" experiments, e.g. analysis of protein folding and conformational transitions, be done in cells? Can the structure and behavior of endogenous and/or non-tagged recombinant proteins be analyzed and altered within the cell or in cellular compartments? How can molecules and their actions be studied mechanistically in tissues and organs? Is personalized cellular biochemistry a reality? This thematic series summarizes recent studies that illustrate some first steps toward successfully answering these modern biochemical questions. The first minireview focuses on utilization of three-dimensional primary enteroids and organoids for mechanistic studies of intestinal biology with molecular resolution. The second minireview describes application of single chain antibodies (nanobodies) for monitoring and regulating protein dynamics in vitro and in cells. The third minireview highlights advances in using NMR spectroscopy for analysis of protein folding and assembly in cells. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Development of classification models for identifying "true" P-glycoprotein (P-gp) inhibitors through inhibition, ATPase activation and monolayer efflux assays.

PubMed

Rapposelli, Simona; Coi, Alessio; Imbriani, Marcello; Bianucci, Anna Maria

2012-01-01

P-glycoprotein (P-gp) is an efflux pump involved in the protection of tissues of several organs by influencing xenobiotic disposition. P-gp plays a key role in multidrug resistance and in the progression of many neurodegenerative diseases. The development of new and more effective therapeutics targeting P-gp thus represents an intriguing challenge in drug discovery. P-gp inhibition may be considered as a valid approach to improve drug bioavailability as well as to overcome drug resistance to many kinds of tumours characterized by the over-expression of this protein. This study aims to develop classification models from a unique dataset of 59 compounds for which there were homogeneous experimental data on P-gp inhibition, ATPase activation and monolayer efflux. For each experiment, the dataset was split into a training and a test set comprising 39 and 20 molecules, respectively. Rational splitting was accomplished using a sphere-exclusion type algorithm. After a two-step (internal/external) validation, the best-performing classification models were used in a consensus predicting task for the identification of compounds named as "true" P-gp inhibitors, i.e., molecules able to inhibit P-gp without being effluxed by P-gp itself and simultaneously unable to activate the ATPase function.

Introducing Kuhn et al.'s paper "Informatics and medicine: from molecules to populations" and invited papers on this special topic.

PubMed

Kulikowski, C A

2008-01-01

To introduce the paper by Kuhn et al. "Informatics and Medicine: From Molecules to Populations" and the papers that follow on this special topic in this issue of Methods of Information in Medicine, which opens a debate on the Kuhn et al. paper's assertions by an international panel of invited researchers in biomedical informatics. An introductory summary and comparative review of the Kuhn et al. paper and the debate papers, with some personal observations. The Kuhn et al. paper makes a strong case for interdisciplinary education in biomedical informatics across institutions at the graduate level, which could be strengthened by analysis of previous relevant interdisciplinary experiences elsewhere, and the challenges they have faced, which point to more pervasive and earlier-stage needs for both education and practice bridging the research and healthcare communities. The experts debating the Kuhn et al. paper strongly and broadly support the key recommendation of developing graduate education in biomedical informatics in a more comprehensive way, yet at the same time make some incisive comments about the limitations of the "positivistic" and excessively technological orientation of the paper, which could benefit from greater attention to the narrative and care-giving aspects of health practice, with more emphasis on its human and social aspects.

Targeting superficial or nodular Basal cell carcinoma with topically formulated small molecule inhibitor of smoothened.

PubMed

Tang, Tracy; Tang, Jean Y; Li, Dongwei; Reich, Mike; Callahan, Christopher A; Fu, Ling; Yauch, Robert L; Wang, Frank; Kotkow, Karen; Chang, Kris S; Shpall, Elana; Wu, Angela; Rubin, Lee L; Marsters, James C; Epstein, Ervin H; Caro, Ivor; de Sauvage, Frederic J

2011-05-15

Inappropriate activation of the Hedgehog (Hh) signaling pathway in skin is critical for the development of basal cell carcinomas (BCC). We have investigated the anti-BCC efficacy of topically-applied CUR61414, an inhibitor of the Hh signal transduction molecule Smoothened. In preclinical studies, we used a depilatory model to evaluate the ability of topical formulations of CUR61414 to repress Hh responsive cells found at the base of hair follicles in normal skin. We also tested the in vivo effects of topical CUR61414 on murine BCCs developed in Ptch1 (+/-) K14-CreER2 p53 fl/fl mice. In a phase I clinical study, we evaluated the safety, tolerability, and efficacy of a multidose regimen of CUR61414 (0.09%, 0.35%, 1.1%, and 3.1%) applied topically to human superficial or nodular BCCs for up to 28 days. In mice, topical CUR61414 significantly inhibited skin Hh signaling, blocked the induction of hair follicle anagen, and shrank existing BCCs. However, we observed no clinical activity of this formulation in human superficial or nodular BCCs in a phase I clinical study. Our data highlight some of the challenges of translating preclinical experience into successful human results for a topical anticancer agent. ©2011 AACR.

Intense pumping and time- and frequency-resolved CARS for driving and tracking structural deformation and recovery of liquid nitromethane molecules

NASA Astrophysics Data System (ADS)

Wang, Chang; Wu, Hong-lin; Song, Yun-fei; He, Xing; Yang, Yan-qiang; Tan, Duo-wang

2015-11-01

A modified CARS technique with an intense nonresonant femtosecond laser is presented to drive the structural deformation of liquid nitromethane molecules and track their structural relaxation process. The CARS spectra reveal that the internal rotation of the molecule can couple with the CN symmetric stretching vibration and the molecules undergo ultrafast structural deformation of the CH3 groups from 'opened umbrella' to 'closed umbrella' shape, and then experience a structural recovery process within 720 fs.

Small-molecule control of protein function through Staudinger reduction

NASA Astrophysics Data System (ADS)

Luo, Ji; Liu, Qingyang; Morihiro, Kunihiko; Deiters, Alexander

2016-11-01

Using small molecules to control the function of proteins in live cells with complete specificity is highly desirable, but challenging. Here we report a small-molecule switch that can be used to control protein activity. The approach uses a phosphine-mediated Staudinger reduction to activate protein function. Genetic encoding of an ortho-azidobenzyloxycarbonyl amino acid using a pyrrolysyl transfer RNA synthetase/tRNACUA pair in mammalian cells enables the site-specific introduction of a small-molecule-removable protecting group into the protein of interest. Strategic placement of this group renders the protein inactive until deprotection through a bioorthogonal Staudinger reduction delivers the active wild-type protein. This developed methodology was applied to the conditional control of several cellular processes, including bioluminescence (luciferase), fluorescence (enhanced green fluorescent protein), protein translocation (nuclear localization sequence), DNA recombination (Cre) and gene editing (Cas9).

Inkjet-Printed Small-Molecule Organic Light-Emitting Diodes: Halogen-Free Inks, Printing Optimization, and Large-Area Patterning.

PubMed

Zhou, Lu; Yang, Lei; Yu, Mengjie; Jiang, Yi; Liu, Cheng-Fang; Lai, Wen-Yong; Huang, Wei

2017-11-22

Manufacturing small-molecule organic light-emitting diodes (OLEDs) via inkjet printing is rather attractive for realizing high-efficiency and long-life-span devices, yet it is challenging. In this paper, we present our efforts on systematical investigation and optimization of the ink properties and the printing process to enable facile inkjet printing of conjugated light-emitting small molecules. Various factors on influencing the inkjet-printed film quality during the droplet generation, the ink spreading on the substrates, and its solidification processes have been systematically investigated and optimized. Consequently, halogen-free inks have been developed and large-area patterning inkjet printing on flexible substrates with efficient blue emission has been successfully demonstrated. Moreover, OLEDs manufactured by inkjet printing the light-emitting small molecules manifested superior performance as compared with their corresponding spin-cast counterparts.

Biomedical application of MALDI mass spectrometry for small-molecule analysis.

PubMed

van Kampen, Jeroen J A; Burgers, Peter C; de Groot, Ronald; Gruters, Rob A; Luider, Theo M

2011-01-01

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is an emerging analytical tool for the analysis of molecules with molar masses below 1,000 Da; that is, small molecules. This technique offers rapid analysis, high sensitivity, low sample consumption, a relative high tolerance towards salts and buffers, and the possibility to store sample on the target plate. The successful application of the technique is, however, hampered by low molecular weight (LMW) matrix-derived interference signals and by poor reproducibility of signal intensities during quantitative analyses. In this review, we focus on the biomedical application of MALDI-MS for the analysis of small molecules and discuss its favorable properties and its challenges as well as strategies to improve the performance of the technique. Furthermore, practical aspects and applications are presented. © 2010 Wiley Periodicals, Inc.

From Artificial Atoms to Nanocrystal Molecules: Preparation and Properties of More Complex Nanostructures

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

Choi, Charina L; Alivisatos, A Paul

2009-10-20

Quantum dots, which have found widespread use in fields such as biomedicine, photovoltaics, and electronics, are often called artificial atoms due to their size-dependent physical properties. Here this analogy is extended to consider artificial nanocrystal molecules, formed from well-defined groupings of plasmonically or electronically coupled single nanocrystals. Just as a hydrogen molecule has properties distinct from two uncoupled hydrogen atoms, a key feature of nanocrystal molecules is that they exhibit properties altered from those of the component nanoparticles due to coupling. The nature of the coupling between nanocrystal atoms and its response to vibrations and deformations of the nanocrystal moleculemore » bonds are of particular interest. We discuss synthetic approaches, predicted and observed physical properties, and prospects and challenges toward this new class of materials.« less

Biased and unbiased strategies to identify biologically active small molecules.

PubMed

Abet, Valentina; Mariani, Angelica; Truscott, Fiona R; Britton, Sébastien; Rodriguez, Raphaël

2014-08-15

Small molecules are central players in chemical biology studies. They promote the perturbation of cellular processes underlying diseases and enable the identification of biological targets that can be validated for therapeutic intervention. Small molecules have been shown to accurately tune a single function of pluripotent proteins in a reversible manner with exceptional temporal resolution. The identification of molecular probes and drugs remains a worthy challenge that can be addressed by the use of biased and unbiased strategies. Hypothesis-driven methodologies employs a known biological target to synthesize complementary hits while discovery-driven strategies offer the additional means of identifying previously unanticipated biological targets. This review article provides a general overview of recent synthetic frameworks that gave rise to an impressive arsenal of biologically active small molecules with unprecedented cellular mechanisms. Copyright © 2014. Published by Elsevier Ltd.

Inferring diffusion in single live cells at the single-molecule level

PubMed Central

Robson, Alex; Burrage, Kevin; Leake, Mark C.

2013-01-01

The movement of molecules inside living cells is a fundamental feature of biological processes. The ability to both observe and analyse the details of molecular diffusion in vivo at the single-molecule and single-cell level can add significant insight into understanding molecular architectures of diffusing molecules and the nanoscale environment in which the molecules diffuse. The tool of choice for monitoring dynamic molecular localization in live cells is fluorescence microscopy, especially so combining total internal reflection fluorescence with the use of fluorescent protein (FP) reporters in offering exceptional imaging contrast for dynamic processes in the cell membrane under relatively physiological conditions compared with competing single-molecule techniques. There exist several different complex modes of diffusion, and discriminating these from each other is challenging at the molecular level owing to underlying stochastic behaviour. Analysis is traditionally performed using mean square displacements of tracked particles; however, this generally requires more data points than is typical for single FP tracks owing to photophysical instability. Presented here is a novel approach allowing robust Bayesian ranking of diffusion processes to discriminate multiple complex modes probabilistically. It is a computational approach that biologists can use to understand single-molecule features in live cells. PMID:23267182

Discovery of Small Molecules that Inhibit the Disordered Protein, p27Kip1

PubMed Central

Iconaru, Luigi I.; Ban, David; Bharatham, Kavitha; Ramanathan, Arvind; Zhang, Weixing; Shelat, Anang A.; Zuo, Jian; Kriwacki, Richard W.

2015-01-01

Disordered proteins are highly prevalent in biological systems, they control myriad signaling and regulatory processes, and their levels and/or cellular localization are often altered in human disease. In contrast to folded proteins, disordered proteins, due to conformational heterogeneity and dynamics, are not considered viable drug targets. We challenged this paradigm by identifying through NMR-based screening small molecules that bound specifically, albeit weakly, to the disordered cell cycle regulator, p27Kip1 (p27). Two groups of molecules bound to sites created by transient clusters of aromatic residues within p27. Conserved chemical features within these two groups of small molecules exhibited complementarity to their binding sites within p27, establishing structure-activity relationships for small molecule:disordered protein interactions. Finally, one compound counteracted the Cdk2/cyclin A inhibitory function of p27 in vitro, providing proof-of-principle that small molecules can inhibit the function of a disordered protein (p27) through sequestration in a conformation incapable of folding and binding to a natural regulatory target (Cdk2/cyclin A). PMID:26507530

Discovery of Small Molecules that Inhibit the Disordered Protein, p27 Kip1

DOE PAGES

Iconaru, Luigi I.; Ban, David; Bharatham, Kavitha; ...

2015-10-28

In disordered proteins we see that they are highly prevalent in biological systems. They control myriad signaling and regulatory processes, and their levels and/or cellular localization are often altered in human disease. In contrast to folded proteins, disordered proteins, due to conformational heterogeneity and dynamics, are not considered viable drug targets. We challenged this paradigm by identifying through NMR-based screening small molecules that bound specifically, albeit weakly, to the disordered cell cycle regulator, p27 Kip1 (p27). Moreover, two groups of molecules bound to sites created by transient clusters of aromatic residues within p27. Conserved chemical features within these two groupsmore » of small molecules exhibited complementarity to their binding sites within p27, establishing structure-activity relationships for small molecule: disordered protein interactions. Finally, one compound counteracted the Cdk2/cyclin A inhibitory function of p27 in vitro, providing proof-of- principle that small molecules can inhibit the function of a disordered protein (p27) through sequestration in a conformation incapable of folding and binding to a natural regulatory target (Cdk2/cyclin A).« less

Identification of vibrational signatures from short chains of interlinked molecule-nanoparticle junctions obtained by inelastic electron tunnelling spectroscopy.

PubMed

Jafri, S H M; Löfås, H; Fransson, J; Blom, T; Grigoriev, A; Wallner, A; Ahuja, R; Ottosson, H; Leifer, K

2013-06-07

Short chains containing a series of metal-molecule-nanoparticle nanojunctions are a nano-material system with the potential to give electrical signatures close to those from single molecule experiments while enabling us to build portable devices on a chip. Inelastic electron tunnelling spectroscopy (IETS) measurements provide one of the most characteristic electrical signals of single and few molecules. In interlinked molecule-nanoparticle (NP) chains containing typically 5-7 molecules in a chain, the spectrum is expected to be a superposition of the vibrational signatures of individual molecules. We have established a stable and reproducible molecule-AuNP multi-junction by placing a few 1,8-octanedithiol (ODT) molecules onto a versatile and portable nanoparticle-nanoelectrode platform and measured for the first time vibrational molecular signatures at complex and coupled few-molecule-NP junctions. From quantum transport calculations, we model the IETS spectra and identify vibrational modes as well as the number of molecules contributing to the electron transport in the measured spectra.

High precision optical spectroscopy and quantum state selected photodissociation of ultracold 88Sr2 molecules in an optical lattice

NASA Astrophysics Data System (ADS)

McDonald, Mickey Patrick

Over the past several decades, rapid progress has been made toward the accurate characterization and control of atoms, made possible largely by the development of narrow-linewidth lasers and techniques for trapping and cooling at ultracold temperatures. Extending this progress to molecules will have exciting implications for chemistry, condensed matter physics, and precision tests of physics beyond the Standard Model. These possibilities are all consequences of the richness of molecular structure, which is governed by physics substantially different from that characterizing atomic structure. This same richness of structure, however, increases the complexity of any molecular experiment manyfold over its atomic counterpart, magnifying the difficulty of everything from trapping and cooling to the comparison of theory with experiment. This thesis describes work performed over the past six years to establish the state of the art in manipulation and quantum control of ultracold molecules. Our molecules are produced via photoassociation of ultracold strontium atoms followed by spontaneous decay to a stable ground state. We describe a thorough set of measurements characterizing the rovibrational structure of very weakly bound (and therefore very large) 88Sr2 molecules from several different perspectives, including determinations of binding energies; linear, quadratic, and higher order Zeeman shifts; transition strengths between bound states; and lifetimes of narrow subradiant states. The physical intuition gained in these experiments applies generally to weakly bound diatomic molecules, and suggests extensive applications in precision measurement and metrology. In addition, we present a detailed analysis of the thermally broadened spectroscopic lineshape of molecules in a non-magic optical lattice trap, showing how such lineshapes can be used to directly determine the temperature of atoms or molecules in situ, addressing a long-standing problem in ultracold physics. Finally, we discuss the measurement of photofragment angular distributions produced by photodissociation, leading to an exploration of quantum-state-resolved ultracold chemistry.

Magnetoassociation of KRb Feshbach molecules

NASA Astrophysics Data System (ADS)

Cumby, Tyler; Perreault, John; Shewmon, Ruth; Jin, Deborah

2010-03-01

I will discuss experiments in which we study the creation of ^40K^87Rb Feshbach molecules via magnetoassociation. We measure the molecule number as a function of the magnetic-field sweep rate through the interspecies Feshbach resonance and explore the dependence of association on the initial atom gas conditions. This study of the Feshbach molecule creation process may be relevant to the production of ultracold polar molecules, where magnetoassociated Feshbach molecules can be a crucial first step [1].[4pt] [1] K.-K. Ni, S. Ospelkaus, M. H. G. de Miranda, A. Peer, B. Neyenhuis, J. J. Zirbel, S. Kotochigova, P. S. Julienne, D. S. Jin, and J. Ye, Science, 2008, 322, 231- 235.

Magnetoassociation of KRb Feshbach molecules

NASA Astrophysics Data System (ADS)

Cumby, Tyler; Perreault, John; Shewmon, Ruth; Jin, Deborah

2010-03-01

I will discuss experiments in which we study the creation of ^40K^87Rb Feshbach molecules via magnetoassociation. We measure the molecule number as a function of the magnetic-field sweep rate through the interspecies Feshbach resonance and explore the dependence of association on the initial atom gas conditions. This study of the Feshbach molecule creation process may be relevant to the production of ultracold polar molecules, where magnetoassociated Feshbach molecules can be a crucial first step [1].[4pt] [1] K.-K. Ni, S. Ospelkaus, M. H. G. de Miranda, A. Peer, B. Neyenhuis, J. J. Zirbel, S. Kotochigova, P. S. Julienne, D. S. Jin, and J. Ye, Science, 2008, 322, 231-235.

Are You Taking the Fastest Route to the RESTAURANT?

PubMed

Perea, Manuel; Marcet, Ana; Vergara-Martínez, Marta

2018-03-01

Most words in books and digital media are written in lowercase. The primacy of this format has been brought out by different experiments showing that common words are identified faster in lowercase (e.g., molecule) than in uppercase (MOLECULE). However, there are common words that are usually written in uppercase (street signs, billboards; e.g., STOP, PHARMACY). We conducted a lexical decision experiment to examine whether the usual letter-case configuration (uppercase vs. lowercase) of common words modulates word identification times. To this aim, we selected 78 molecule-type words and 78 PHARMACY-type words that were presented in lowercase or uppercase. For molecule-type words, the lowercase format elicited faster responses than the uppercase format, whereas this effect was absent for PHARMACY-type words. This pattern of results suggests that the usual letter configuration of common words plays an important role during visual word processing.

Single-molecule detection of dihydroazulene photo-thermal reaction using break junction technique

NASA Astrophysics Data System (ADS)

Huang, Cancan; Jevric, Martyn; Borges, Anders; Olsen, Stine T.; Hamill, Joseph M.; Zheng, Jue-Ting; Yang, Yang; Rudnev, Alexander; Baghernejad, Masoud; Broekmann, Peter; Petersen, Anne Ugleholdt; Wandlowski, Thomas; Mikkelsen, Kurt V.; Solomon, Gemma C.; Brøndsted Nielsen, Mogens; Hong, Wenjing

2017-05-01

Charge transport by tunnelling is one of the most ubiquitous elementary processes in nature. Small structural changes in a molecular junction can lead to significant difference in the single-molecule electronic properties, offering a tremendous opportunity to examine a reaction on the single-molecule scale by monitoring the conductance changes. Here, we explore the potential of the single-molecule break junction technique in the detection of photo-thermal reaction processes of a photochromic dihydroazulene/vinylheptafulvene system. Statistical analysis of the break junction experiments provides a quantitative approach for probing the reaction kinetics and reversibility, including the occurrence of isomerization during the reaction. The product ratios observed when switching the system in the junction does not follow those observed in solution studies (both experiment and theory), suggesting that the junction environment was perturbing the process significantly. This study opens the possibility of using nano-structured environments like molecular junctions to tailor product ratios in chemical reactions.

The successful merger of theoretical thermochemistry with fragment-based methods in quantum chemistry.

PubMed

Ramabhadran, Raghunath O; Raghavachari, Krishnan

2014-12-16

CONSPECTUS: Quantum chemistry and electronic structure theory have proven to be essential tools to the experimental chemist, in terms of both a priori predictions that pave the way for designing new experiments and rationalizing experimental observations a posteriori. Translating the well-established success of electronic structure theory in obtaining the structures and energies of small chemical systems to increasingly larger molecules is an exciting and ongoing central theme of research in quantum chemistry. However, the prohibitive computational scaling of highly accurate ab initio electronic structure methods poses a fundamental challenge to this research endeavor. This scenario necessitates an indirect fragment-based approach wherein a large molecule is divided into small fragments and is subsequently reassembled to compute its energy accurately. In our quest to further reduce the computational expense associated with the fragment-based methods and overall enhance the applicability of electronic structure methods to large molecules, we realized that the broad ideas involved in a different area, theoretical thermochemistry, are transferable to the area of fragment-based methods. This Account focuses on the effective merger of these two disparate frontiers in quantum chemistry and how new concepts inspired by theoretical thermochemistry significantly reduce the total number of electronic structure calculations needed to be performed as part of a fragment-based method without any appreciable loss of accuracy. Throughout, the generalized connectivity based hierarchy (CBH), which we developed to solve a long-standing problem in theoretical thermochemistry, serves as the linchpin in this merger. The accuracy of our method is based on two strong foundations: (a) the apt utilization of systematic and sophisticated error-canceling schemes via CBH that result in an optimal cutting scheme at any given level of fragmentation and (b) the use of a less expensive second layer of electronic structure method to recover all the missing long-range interactions in the parent large molecule. Overall, the work featured here dramatically decreases the computational expense and empowers the execution of very accurate ab initio calculations (gold-standard CCSD(T)) on large molecules and thereby facilitates sophisticated electronic structure applications to a wide range of important chemical problems.

Study of open systems with molecules in isotropic liquids

NASA Astrophysics Data System (ADS)

Kondo, Yasushi; Matsuzaki, Masayuki

2018-05-01

We are interested in dynamics of a system in an environment, or an open system. Such phenomena as crossover from Markovian to non-Markovian relaxation and thermal equilibration are of our interest. Open systems have experimentally been studied with ultra cold atoms, ions in traps, optics, and cold electric circuits because well-isolated systems can be prepared here and thus the effects of environments can be controlled. We point out that some molecules solved in isotropic liquid are well isolated and thus they can also be employed for studying open systems in Nuclear Magnetic Resonance (NMR) experiments. First, we provide a short review on related phenomena of open systems that helps readers to understand our motivation. We, then, present two experiments as examples of our approach with molecules in isotropic liquids. Crossover from Markovian to non-Markovian relaxation was realized in one NMR experiment, while relaxation-like phenomena were observed in approximately isolated systems in the other.

Turning limited experimental information into 3D models of RNA.

PubMed

Flores, Samuel Coulbourn; Altman, Russ B

2010-09-01

Our understanding of RNA functions in the cell is evolving rapidly. As for proteins, the detailed three-dimensional (3D) structure of RNA is often key to understanding its function. Although crystallography and nuclear magnetic resonance (NMR) can determine the atomic coordinates of some RNA structures, many 3D structures present technical challenges that make these methods difficult to apply. The great flexibility of RNA, its charged backbone, dearth of specific surface features, and propensity for kinetic traps all conspire with its long folding time, to challenge in silico methods for physics-based folding. On the other hand, base-pairing interactions (either in runs to form helices or isolated tertiary contacts) and motifs are often available from relatively low-cost experiments or informatics analyses. We present RNABuilder, a novel code that uses internal coordinate mechanics to satisfy user-specified base pairing and steric forces under chemical constraints. The code recapitulates the topology and characteristic L-shape of tRNA and obtains an accurate noncrystallographic structure of the Tetrahymena ribozyme P4/P6 domain. The algorithm scales nearly linearly with molecule size, opening the door to the modeling of significantly larger structures.

Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description.

PubMed

Spyrakis, Francesca; Cavasotto, Claudio N

2015-10-01

Structure-based virtual screening is currently an established tool in drug lead discovery projects. Although in the last years the field saw an impressive progress in terms of algorithm development, computational performance, and retrospective and prospective applications in ligand identification, there are still long-standing challenges where further improvement is needed. In this review, we consider the conceptual frame, state-of-the-art and recent developments of three critical "structural" issues in structure-based drug lead discovery: the use of homology modeling to accurately model the binding site when no experimental structures are available, the necessity of accounting for the dynamics of intrinsically flexible systems as proteins, and the importance of considering active site water molecules in lead identification and optimization campaigns. Copyright © 2015 Elsevier Inc. All rights reserved.

Resolving metal-molecule interfaces at single-molecule junctions

NASA Astrophysics Data System (ADS)

Komoto, Yuki; Fujii, Shintaro; Nakamura, Hisao; Tada, Tomofumi; Nishino, Tomoaki; Kiguchi, Manabu

2016-05-01

Electronic and structural detail at the electrode-molecule interface have a significant influence on charge transport across molecular junctions. Despite the decisive role of the metal-molecule interface, a complete electronic and structural characterization of the interface remains a challenge. This is in no small part due to current experimental limitations. Here, we present a comprehensive approach to obtain a detailed description of the metal-molecule interface in single-molecule junctions, based on current-voltage (I-V) measurements. Contrary to conventional conductance studies, this I-V approach provides a correlated statistical description of both, the degree of electronic coupling across the metal-molecule interface, and the energy alignment between the conduction orbital and the Fermi level of the electrode. This exhaustive statistical approach was employed to study single-molecule junctions of 1,4-benzenediamine (BDA), 1,4-butanediamine (C4DA), and 1,4-benzenedithiol (BDT). A single interfacial configuration was observed for both BDA and C4DA junctions, while three different interfacial arrangements were resolved for BDT. This multiplicity is due to different molecular adsorption sites on the Au surface namely on-top, hollow, and bridge. Furthermore, C4DA junctions present a fluctuating I-V curve arising from the greater conformational freedom of the saturated alkyl chain, in sharp contrast with the rigid aromatic backbone of both BDA and BDT.

The Challenging Experience Questionnaire: Characterization of challenging experiences with psilocybin mushrooms

PubMed Central

Barrett, Frederick S.; Bradstreet, Matthew P.; Leoutsakos, Jeannie-Marie S.; Johnson, Matthew W.; Griffiths, Roland R.

2017-01-01

Acute adverse psychological reactions to classic hallucinogens (“bad trips”, or “challenging experiences”), while usually benign with proper screening, preparation, and support in controlled settings, remain a safety concern in uncontrolled settings (such as illicit use contexts). Anecdotal and case reports suggest potential adverse acute symptoms including affective (panic, depressed mood), cognitive (confusion, feelings of losing sanity), and somatic (nausea, heart palpitation) symptoms. Responses to items from several hallucinogen-sensitive questionnaires (Hallucinogen Rating Scale, the States of Consciousness Questionnaire, and the 5-Dimensional Altered States of Consciousness questionnaire) in an internet survey of challenging experiences with the classic hallucinogen psilocybin were used to construct and validate a Challenging Experience Questionnaire (CEQ). The stand-alone CEQ was then validated in a separate sample. Seven CEQ factors (grief, fear, death, insanity, isolation, physical distress, and paranoia) provide a phenomenological profile of challenging aspects of experiences with psilocybin. Factor scores were associated with the difficulty, meaningfulness, spiritual significance, and change in well-being attributed to the challenging experiences. The factor structure did not differ based on gender or prior struggle with anxiety or depression. The CEQ provides a basis for future investigation of predictors and outcomes of challenging experiences with psilocybin, and should be explored as a measure of challenging experiences with the broad class of classic hallucinogens. PMID:27856683

Therapeutic approaches to preventing cell death in Huntington disease.

PubMed

Kaplan, Anna; Stockwell, Brent R

2012-12-01

Neurodegenerative diseases affect the lives of millions of patients and their families. Due to the complexity of these diseases and our limited understanding of their pathogenesis, the design of therapeutic agents that can effectively treat these diseases has been challenging. Huntington disease (HD) is one of several neurological disorders with few therapeutic options. HD, like numerous other neurodegenerative diseases, involves extensive neuronal cell loss. One potential strategy to combat HD and other neurodegenerative disorders is to intervene in the execution of neuronal cell death. Inhibiting neuronal cell death pathways may slow the development of neurodegeneration. However, discovering small molecule inhibitors of neuronal cell death remains a significant challenge. Here, we review candidate therapeutic targets controlling cell death mechanisms that have been the focus of research in HD, as well as an emerging strategy that has been applied to developing small molecule inhibitors-fragment-based drug discovery (FBDD). FBDD has been successfully used in both industry and academia to identify selective and potent small molecule inhibitors, with a focus on challenging proteins that are not amenable to traditional high-throughput screening approaches. FBDD has been used to generate potent leads, pre-clinical candidates, and has led to the development of an FDA approved drug. This approach can be valuable for identifying modulators of cell-death-regulating proteins; such compounds may prove to be the key to halting the progression of HD and other neurodegenerative disorders. Copyright © 2012 Elsevier Ltd. All rights reserved.

Continuous centrifuge decelerator for polar molecules.

PubMed

Chervenkov, S; Wu, X; Bayerl, J; Rohlfes, A; Gantner, T; Zeppenfeld, M; Rempe, G

2014-01-10

Producing large samples of slow molecules from thermal-velocity ensembles is a formidable challenge. Here we employ a centrifugal force to produce a continuous molecular beam with a high flux at near-zero velocities. We demonstrate deceleration of three electrically guided molecular species, CH3F, CF3H, and CF3CCH, with input velocities of up to 200  m s(-1) to obtain beams with velocities below 15  m s(-1) and intensities of several 10(9)  mm(-2) s(-1). The centrifuge decelerator is easy to operate and can, in principle, slow down any guidable particle. It has the potential to become a standard technique for continuous deceleration of molecules.

Reverse Transcriptase Activity in Mature Spermatozoa of Mouse

PubMed Central

Giordano, Roberto; Magnano, Anna Rosa; Zaccagnini, Germana; Pittoggi, Carmine; Moscufo, Nicola; Lorenzini, Rodolfo; Spadafora, Corrado

2000-01-01

We show here that a reverse transcriptase (RT) activity is present in murine epididymal spermatozoa. Sperm cells incubated with human poliovirus RNA can take up exogenous RNA molecules and internalize them in nuclei. Direct PCR amplification of DNA extracted from RNA-incubated spermatozoa indicate that poliovirus RNA is reverse-transcribed in cDNA fragments. PCR analysis of two-cell embryos shows that poliovirus RNA-challenged spermatozoa transfer retrotranscribed cDNA molecules into eggs during in vitro fertilization. Finally, RT molecules can be visualized on sperm nuclear scaffolds by immunogold electron microscopy. These results, therefore, reveal a novel metabolic function in spermatozoa, which may play a role during early embryonic development. PMID:10725323

Single Molecule Approaches in RNA-Protein Interactions.

PubMed

Serebrov, Victor; Moore, Melissa J

RNA-protein interactions govern every aspect of RNA metabolism, and aberrant RNA-binding proteins are the cause of hundreds of genetic diseases. Quantitative measurements of these interactions are necessary in order to understand mechanisms leading to diseases and to develop efficient therapies. Existing methods of RNA-protein interactome capture can afford a comprehensive snapshot of RNA-protein interaction networks but lack the ability to characterize the dynamics of these interactions. As all ensemble methods, their resolution is also limited by statistical averaging. Here we discuss recent advances in single molecule techniques that have the potential to tackle these challenges. We also provide a thorough overview of single molecule colocalization microscopy and the essential protein and RNA tagging and detection techniques.

Reaction-based small-molecule fluorescent probes for chemoselective bioimaging

PubMed Central

Chan, Jefferson; Dodani, Sheel C.; Chang, Christopher J.

2014-01-01

The dynamic chemical diversity of elements, ions and molecules that form the basis of life offers both a challenge and an opportunity for study. Small-molecule fluorescent probes can make use of selective, bioorthogonal chemistries to report on specific analytes in cells and in more complex biological specimens. These probes offer powerful reagents to interrogate the physiology and pathology of reactive chemical species in their native environments with minimal perturbation to living systems. This Review presents a survey of tools and tactics for using such probes to detect biologically important chemical analytes. We highlight design criteria for effective chemical tools for use in biological applications as well as gaps for future exploration. PMID:23174976

Supramolecular Approaches to Nanoscale Morphological Control in Organic Solar Cells

PubMed Central

Haruk, Alexander M.; Mativetsky, Jeffrey M.

2015-01-01

Having recently surpassed 10% efficiency, solar cells based on organic molecules are poised to become a viable low-cost clean energy source with the added advantages of mechanical flexibility and light weight. The best-performing organic solar cells rely on a nanostructured active layer morphology consisting of a complex organization of electron donating and electron accepting molecules. Although much progress has been made in designing new donor and acceptor molecules, rational control over active layer morphology remains a central challenge. Long-term device stability is another important consideration that needs to be addressed. This review highlights supramolecular strategies for generating highly stable nanostructured organic photovoltaic active materials by design. PMID:26110382

Physical Investigations of Small Particles: (I) Aerosol Particle Charging and Flux Enhancement and (II) Whispering Gallery Mode Sensing

NASA Astrophysics Data System (ADS)

Lopez-Yglesias, Xerxes

Part I: Particles are a key feature of planetary atmospheres. On Earth they represent the greatest source of uncertainty in the global energy budget. This uncertainty can be addressed by making more measurement, by improving the theoretical analysis of measurements, and by better modeling basic particle nucleation and initial particle growth within an atmosphere. This work will focus on the latter two methods of improvement. Uncertainty in measurements is largely due to particle charging. Accurate descriptions of particle charging are challenging because one deals with particles in a gas as opposed to a vacuum, so different length scales come into play. Previous studies have considered the effects of transition between the continuum and kinetic regime and the effects of two and three body interactions within the kinetic regime. These studies, however, use questionable assumptions about the charging process which resulted in skewed observations, and bias in the proposed dynamics of aerosol particles. These assumptions affect both the ions and particles in the system. Ions are assumed to be point monopoles that have a single characteristic speed rather than follow a distribution. Particles are assumed to be perfect conductors that have up to five elementary charges on them. The effects of three body interaction, ion-molecule-particle, are also overestimated. By revising this theory so that the basic physical attributes of both ions and particles and their interactions are better represented, we are able to make more accurate predictions of particle charging in both the kinetic and continuum regimes. The same revised theory that was used above to model ion charging can also be applied to the flux of neutral vapor phase molecules to a particle or initial cluster. Using these results we can model the vapor flux to a neutral or charged particle due to diffusion and electromagnetic interactions. In many classical theories currently applied to these models, the finite size of the molecule and the electromagnetic interaction between the molecule and particle, especially for the neutral particle case, are completely ignored, or, as is often the case for a permanent dipole vapor species, strongly underestimated. Comparing our model to these classical models we determine an "enhancement factor" to characterize how important the addition of these physical parameters and processes is to the understanding of particle nucleation and growth. Part II: Whispering gallery mode (WGM) optical biosensors are capable of extraordinarily sensitive specific and non-specific detection of species suspended in a gas or fluid. Recent experimental results suggest that these devices may attain single-molecule sensitivity to protein solutions in the form of stepwise shifts in their resonance wavelength, lambdaR, but present sensor models predict much smaller steps than were reported. This study examines the physical interaction between a WGM sensor and a molecule adsorbed to its surface, exploring assumptions made in previous efforts to model WGM sensor behavior, and describing computational schemes that model the experiments for which single protein sensitivity was reported. The resulting model is used to simulate sensor performance, within constraints imposed by the limited material property data. On this basis, we conclude that nonlinear optical effects would be needed to attain the reported sensitivity, and that, in the experiments for which extreme sensitivity was reported, a bound protein experiences optical energy fluxes too high for such effects to be ignored.

A Fragment-Based Method of Creating Small-Molecule Libraries to Target the Aggregation of Intrinsically Disordered Proteins.

PubMed

Joshi, Priyanka; Chia, Sean; Habchi, Johnny; Knowles, Tuomas P J; Dobson, Christopher M; Vendruscolo, Michele

2016-03-14

The aggregation process of intrinsically disordered proteins (IDPs) has been associated with a wide range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Currently, however, no drug in clinical use targets IDP aggregation. To facilitate drug discovery programs in this important and challenging area, we describe a fragment-based approach of generating small-molecule libraries that target specific IDPs. The method is based on the use of molecular fragments extracted from compounds reported in the literature to inhibit of the aggregation of IDPs. These fragments are used to screen existing large generic libraries of small molecules to form smaller libraries specific for given IDPs. We illustrate this approach by describing three distinct small-molecule libraries to target, Aβ, tau, and α-synuclein, which are three IDPs implicated in Alzheimer's and Parkinson's diseases. The strategy described here offers novel opportunities for the identification of effective molecular scaffolds for drug discovery for neurodegenerative disorders and to provide insights into the mechanism of small-molecule binding to IDPs.

Simultaneous optimization of biomolecular energy function on features from small molecules and macromolecules

PubMed Central

Park, Hahnbeom; Bradley, Philip; Greisen, Per; Liu, Yuan; Mulligan, Vikram Khipple; Kim, David E.; Baker, David; DiMaio, Frank

2017-01-01

Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking, have been parameterized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data. The energy function improves performance in a wide range of protein structure prediction challenges, including monomeric structure prediction, protein-protein and protein-ligand docking, protein sequence design, and prediction of the free energy changes by mutation, while reasonably recapitulating small-molecule thermodynamic properties. PMID:27766851

Getting Across the Cell Membrane: An Overview for Small Molecules, Peptides, and Proteins

PubMed Central

Yang, Nicole J.; Hinner, Marlon J.

2016-01-01

The ability to efficiently access cytosolic proteins is desired in both biological research and medicine. However, targeting intracellular proteins is often challenging, because to reach the cytosol, exogenous molecules must first traverse the cell membrane. This review provides a broad overview of how certain molecules are thought to cross this barrier, and what kinds of approaches are being made to enhance the intracellular delivery of those that are impermeable. We first discuss rules that govern the passive permeability of small molecules across the lipid membrane, and mechanisms of membrane transport that have evolved in nature for certain metabolites, peptides, and proteins. Then, we introduce design strategies that have emerged in the development of small molecules and peptides with improved permeability. Finally, intracellular delivery systems that have been engineered for protein payloads are surveyed. Viewpoints from varying disciplines have been brought together to provide a cohesive overview of how the membrane barrier is being overcome. PMID:25560066

Effect of Ring Strain on the Charge Transport of a Robust Norbornadiene–Quadricyclane-Based Molecular Photoswitch

PubMed Central

2017-01-01

Integrating functional molecules into single-molecule devices is a key step toward the realization of future computing machines based on the smallest possible components. In this context, photoswitching molecules that can make a transition between high and low conductivity in response to light are attractive candidates. Here we present the synthesis and conductance properties of a new type of robust molecular photothermal switch based on the norbornadiene (NB)–quadricyclane (QC) system. The transport through the molecule in the ON state is dominated by a pathway through the π-conjugated system, which is no longer available when the system is switched to the OFF state. Interestingly, in the OFF state we find that the same pathway contributes only 12% to the transport properties. We attribute this observation to the strained tetrahedral geometry of the QC. These results challenge the prevailing assumption that current will simply flow through the shortest through-bond path in a molecule. PMID:28408968

Identifying the preferred RNA motifs and chemotypes that interact by probing millions of combinations.

PubMed

Tran, Tuan; Disney, Matthew D

2012-01-01

RNA is an important therapeutic target but information about RNA-ligand interactions is limited. Here, we report a screening method that probes over 3,000,000 combinations of RNA motif-small molecule interactions to identify the privileged RNA structures and chemical spaces that interact. Specifically, a small molecule library biased for binding RNA was probed for binding to over 70,000 unique RNA motifs in a high throughput solution-based screen. The RNA motifs that specifically bind each small molecule were identified by microarray-based selection. In this library-versus-library or multidimensional combinatorial screening approach, hairpin loops (among a variety of RNA motifs) were the preferred RNA motif space that binds small molecules. Furthermore, it was shown that indole, 2-phenyl indole, 2-phenyl benzimidazole and pyridinium chemotypes allow for specific recognition of RNA motifs. As targeting RNA with small molecules is an extremely challenging area, these studies provide new information on RNA-ligand interactions that has many potential uses.

Identifying the Preferred RNA Motifs and Chemotypes that Interact by Probing Millions of Combinations

PubMed Central

Tran, Tuan; Disney, Matthew D.

2012-01-01

RNA is an important therapeutic target but information about RNA-ligand interactions is limited. Here we report a screening method that probes over 3,000,000 combinations of RNA motif-small molecule interactions to identify the privileged RNA structures and chemical spaces that interact. Specifically, a small molecule library biased for binding RNA was probed for binding to over 70,000 unique RNA motifs in a high throughput solution-based screen. The RNA motifs that specifically bind each small molecule were identified by microarray-based selection. In this library-versus-library or multidimensional combinatorial screening approach, hairpin loops (amongst a variety of RNA motifs) were the preferred RNA motif space that binds small molecules. Furthermore, it was shown that indole, 2-phenyl indole, 2-phenyl benzimidazole, and pyridinium chemotypes allow for specific recognition of RNA motifs. Since targeting RNA with small molecules is an extremely challenging area, these studies provide new information on RNA-ligand interactions that has many potential uses. PMID:23047683

Bioorthogonal cyclization-mediated in situ self-assembly of small-molecule probes for imaging caspase activity in vivo

NASA Astrophysics Data System (ADS)

Ye, Deju; Shuhendler, Adam J.; Cui, Lina; Tong, Ling; Tee, Sui Seng; Tikhomirov, Grigory; Felsher, Dean W.; Rao, Jianghong

2014-06-01

Directed self-assembly of small molecules in living systems could enable a myriad of applications in biology and medicine, and already this has been used widely to synthesize supramolecules and nano/microstructures in solution and in living cells. However, controlling the self-assembly of synthetic small molecules in living animals is challenging because of the complex and dynamic in vivo physiological environment. Here we employ an optimized first-order bioorthogonal cyclization reaction to control the self-assembly of a fluorescent small molecule, and demonstrate its in vivo applicability by imaging caspase-3/7 activity in human tumour xenograft mouse models of chemotherapy. The fluorescent nanoparticles assembled in situ were imaged successfully in both apoptotic cells and tumour tissues using three-dimensional structured illumination microscopy. This strategy combines the advantages offered by small molecules with those of nanomaterials and should find widespread use for non-invasive imaging of enzyme activity in vivo.

High-Frequency Electron Paramagnetic Resonance Spectroscopy of Nitroxide-Functionalized Nanodiamonds in Aqueous Solution.

PubMed

Akiel, R D; Stepanov, V; Takahashi, S

2017-06-01

Nanodiamond (ND) is an attractive class of nanomaterial for fluorescent labeling, magnetic sensing of biological molecules, and targeted drug delivery. Many of those applications require tethering of target biological molecules on the ND surface. Even though many approaches have been developed to attach macromolecules to the ND surface, it remains challenging to characterize dynamics of tethered molecule. Here, we show high-frequency electron paramagnetic resonance (HF EPR) spectroscopy of nitroxide-functionalized NDs. Nitroxide radical is a commonly used spin label to investigate dynamics of biological molecules. In the investigation, we developed a sample holder to overcome water absorption of HF microwave. Then, we demonstrated HF EPR spectroscopy of nitroxide-functionalized NDs in aqueous solution and showed clear spectral distinction of ND and nitroxide EPR signals. Moreover, through EPR spectral analysis, we investigate dynamics of nitroxide radicals on the ND surface. The demonstration sheds light on the use of HF EPR spectroscopy to investigate biological molecule-functionalized nanoparticles.

Delivery of large biopharmaceuticals from cardiovascular stents: a review

PubMed Central

Takahashi, Hironobu; Letourneur, Didier; Grainger, David W.

2008-01-01

This review focuses on the new and emerging large-molecule bioactive agents delivered from stent surfaces in drug-eluting stents (DES) to inhibit vascular restenosis in the context of interventional cardiology. New therapeutic agents representing proteins, nucleic acids (small interfering RNAs and large DNA plasmids), viral delivery vectors and even engineered cell therapies require specific delivery designs distinct from traditional smaller molecule approaches on DES. While small molecules are currently the clinical standard for coronary stenting, extension of the DES to other lesion types, peripheral vasculature and non-vasculature therapies will seek to deliver an increasingly sophisticated armada of drug types. This review describes many of the larger molecule and biopharmaceutical approaches reported recently for stent-based delivery with the challenges associated with formulating and delivering these drug classes compared to the current small molecule drugs. It also includes perspectives on possible future applications that may improve safety and efficacy and facilitate diversification of the DES to other clinical applications. PMID:17929968

A Computational Study of the Rheology and Structure of Surfactant Covered Droplets

NASA Astrophysics Data System (ADS)

Maia, Joao; Boromand, Arman; Jamali, Safa

2015-11-01

The use of different types of surface-active agents is ubiquitous practice in different industrial applications ranging from cosmetic and food industries to polymeric nano-composite and blends. This allows stable multiphasic systems like foams and emulsions to be produced. Stability and shelf-life of those products are directly determined by the efficiency of the surfactant molecules. Although the effect of molecular configuration of the surface-active molecules on the planar interfaces has been studied both experimentally and computationally, it remains challenging to track the efficiency and effectiveness of different surfactant molecules on curved interfaces. In this study we address this gap by using Dissipative Particle Dynamics, to study the effectiveness and efficiency of different surfactant molecules (linear vs. branched) on a curved interface in equilibrium and far from equilibrium. In particular, we are interested to relate interfacial properties of the surface covered droplets and its dynamics to the molecular configuration of the surface active molecules under equilibrium and far from equilibrium condition.

Application of encoded library technology (ELT) to a protein-protein interaction target: discovery of a potent class of integrin lymphocyte function-associated antigen 1 (LFA-1) antagonists.

PubMed

Kollmann, Christopher S; Bai, Xiaopeng; Tsai, Ching-Hsuan; Yang, Hongfang; Lind, Kenneth E; Skinner, Steven R; Zhu, Zhengrong; Israel, David I; Cuozzo, John W; Morgan, Barry A; Yuki, Koichi; Xie, Can; Springer, Timothy A; Shimaoka, Motomu; Evindar, Ghotas

2014-04-01

The inhibition of protein-protein interactions remains a challenge for traditional small molecule drug discovery. Here we describe the use of DNA-encoded library technology for the discovery of small molecules that are potent inhibitors of the interaction between lymphocyte function-associated antigen 1 and its ligand intercellular adhesion molecule 1. A DNA-encoded library with a potential complexity of 4.1 billion compounds was exposed to the I-domain of the target protein and the bound ligands were affinity selected, yielding an enriched small-molecule hit family. Compounds representing this family were synthesized without their DNA encoding moiety and found to inhibit the lymphocyte function-associated antigen 1/intercellular adhesion molecule-1 interaction with submicromolar potency in both ELISA and cell adhesion assays. Re-synthesized compounds conjugated to DNA or a fluorophore were demonstrated to bind to cells expressing the target protein. Copyright © 2014 Elsevier Ltd. All rights reserved.

Imaging and Force Recognition of Single Molecular Behaviors Using Atomic Force Microscopy

PubMed Central

Li, Mi; Dang, Dan; Liu, Lianqing; Xi, Ning; Wang, Yuechao

2017-01-01

The advent of atomic force microscopy (AFM) has provided a powerful tool for investigating the behaviors of single native biological molecules under physiological conditions. AFM can not only image the conformational changes of single biological molecules at work with sub-nanometer resolution, but also sense the specific interactions of individual molecular pair with piconewton force sensitivity. In the past decade, the performance of AFM has been greatly improved, which makes it widely used in biology to address diverse biomedical issues. Characterizing the behaviors of single molecules by AFM provides considerable novel insights into the underlying mechanisms guiding life activities, contributing much to cell and molecular biology. In this article, we review the recent developments of AFM studies in single-molecule assay. The related techniques involved in AFM single-molecule assay were firstly presented, and then the progress in several aspects (including molecular imaging, molecular mechanics, molecular recognition, and molecular activities on cell surface) was summarized. The challenges and future directions were also discussed. PMID:28117741

Single-molecule electronics: Cooling individual vibrational modes by the tunneling current.

PubMed

Lykkebo, Jacob; Romano, Giuseppe; Gagliardi, Alessio; Pecchia, Alessandro; Solomon, Gemma C

2016-03-21

Electronic devices composed of single molecules constitute the ultimate limit in the continued downscaling of electronic components. A key challenge for single-molecule electronics is to control the temperature of these junctions. Controlling heating and cooling effects in individual vibrational modes can, in principle, be utilized to increase stability of single-molecule junctions under bias, to pump energy into particular vibrational modes to perform current-induced reactions, or to increase the resolution in inelastic electron tunneling spectroscopy by controlling the life-times of phonons in a molecule by suppressing absorption and external dissipation processes. Under bias the current and the molecule exchange energy, which typically results in heating of the molecule. However, the opposite process is also possible, where energy is extracted from the molecule by the tunneling current. Designing a molecular "heat sink" where a particular vibrational mode funnels heat out of the molecule and into the leads would be very desirable. It is even possible to imagine how the vibrational energy of the other vibrational modes could be funneled into the "cooling mode," given the right molecular design. Previous efforts to understand heating and cooling mechanisms in single molecule junctions have primarily been concerned with small models, where it is unclear which molecular systems they correspond to. In this paper, our focus is on suppressing heating and obtaining current-induced cooling in certain vibrational modes. Strategies for cooling vibrational modes in single-molecule junctions are presented, together with atomistic calculations based on those strategies. Cooling and reduced heating are observed for two different cooling schemes in calculations of atomistic single-molecule junctions.

Low-temperature Condensation of Carbon

NASA Astrophysics Data System (ADS)

Krasnokutski, S. A.; Goulart, M.; Gordon, E. B.; Ritsch, A.; Jäger, C.; Rastogi, M.; Salvenmoser, W.; Henning, Th.; Scheier, P.

2017-10-01

Two different types of experiments were performed. In the first experiment, we studied the low-temperature condensation of vaporized graphite inside bulk liquid helium, while in the second experiment, we studied the condensation of single carbon atoms together with H2, H2O, and CO molecules inside helium nanodroplets. The condensation of vaporized graphite leads to the formation of partially graphitized carbon, which indicates high temperatures, supposedly higher than 1000°C, during condensation. Possible underlying processes responsible for the instant rise in temperature during condensation are discussed. This suggests that such processes cause the presence of partially graphitized carbon dust formed by low-temperature condensation in the diffuse interstellar medium. Alternatively, in the denser regions of the ISM, the condensation of carbon atoms together with the most abundant interstellar molecules (H2, H2O, and CO), leads to the formation of complex organic molecules (COMs) and finally organic polymers. Water molecules were found not to be involved directly in the reaction network leading to the formation of COMs. It was proposed that COMs are formed via the addition of carbon atoms to H2 and CO molecules ({{C}}+{{{H}}}2\\to {HCH},{HCH}+{CO}\\to {{OCCH}}2). Due to the involvement of molecular hydrogen, the formation of COMs by carbon addition reactions should be more efficient at high extinctions compared with the previously proposed reaction scheme with atomic hydrogen.

Multiscale investigation of chemical interference in proteins

NASA Astrophysics Data System (ADS)

Samiotakis, Antonios; Homouz, Dirar; Cheung, Margaret S.

2010-05-01

We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in better exploring the energy landscape of a small protein under chemical interference such as chemical denaturation. An excessive amount of water molecules in all-atomistic molecular dynamics simulations often negatively impacts the sampling efficiency of some advanced sampling techniques such as the replica exchange method and it makes the investigation of chemical interferences on protein dynamics difficult. Thus, there is a need to develop an effective strategy that focuses on sampling structural changes in protein conformations rather than solvent molecule fluctuations. In this work, we address this issue by devising a multiscale simulation scheme (MultiSCAAL) that bridges the gap between all-atomistic molecular dynamics simulation and coarse-grained molecular simulation. The two key features of this scheme are the Boltzmann inversion and a protein atomistic reconstruction method we previously developed (SCAAL). Using MultiSCAAL, we were able to enhance the sampling efficiency of proteins solvated by explicit water molecules. Our method has been tested on the folding energy landscape of a small protein Trp-cage with explicit solvent under 8M urea using both the all-atomistic replica exchange molecular dynamics and MultiSCAAL. We compared computational analyses on ensemble conformations of Trp-cage with its available experimental NOE distances. The analysis demonstrated that conformations explored by MultiSCAAL better agree with the ones probed in the experiments because it can effectively capture the changes in side-chain orientations that can flip out of the hydrophobic pocket in the presence of urea and water molecules. In this regard, MultiSCAAL is a promising and effective sampling scheme for investigating chemical interference which presents a great challenge when modeling protein interactions in vivo.

Reactions of Ground State Nitrogen Atoms N(4S) with Astrochemically-Relevant Molecules on Interstellar Dusts

NASA Astrophysics Data System (ADS)

Krim, Lahouari; Nourry, Sendres

2015-06-01

In the last few years, ambitious programs were launched to probe the interstellar medium always more accurately. One of the major challenges of these missions remains the detection of prebiotic compounds and the understanding of reaction pathways leading to their formation. These complex heterogeneous reactions mainly occur on icy dust grains, and their studies require the coupling of laboratory experiments mimicking the extreme conditions of extreme cold and dilute media. For that purpose, we have developed an original experimental approach that combine the study of heterogeneous reactions (by exposing neutral molecules adsorbed on ice to non-energetic radicals H, OH, N...) and a neon matrix isolation study at very low temperatures, which is of paramount importance to isolate and characterize highly reactive reaction intermediates. Such experimental approach has already provided answers to many questions raised about some astrochemically-relevant reactions occurring in the ground state on the surface of dust grain ices in dense molecular clouds. The aim of this new present work is to show the implication of ground state atomic nitrogen on hydrogen atom abstraction reactions from some astrochemically-relevant species, at very low temperatures (3K-20K), without providing any external energy. Under cryogenic temperatures and with high barrier heights, such reactions involving N(4S) nitrogen atoms should not occur spontaneously and require an initiating energy. However, the detection of some radicals species as byproducts, in our solid samples left in the dark for hours at 10K, proves that hydrogen abstraction reactions involving ground state N(4S) nitrogen atoms may occur in solid phase at cryogenic temperatures. Our results show the efficiency of radical species formation stemming from non-energetic N-atoms and astrochemically-relevant molecules. We will then discuss how such reactions, involving nitrogen atoms in their ground states, might be the first key step towards complex organic molecules production in the interstellar medium.

Insights into chromatographic separation using core-shell metal-organic frameworks: Size exclusion and polarity effects.

PubMed

Qin, Weiwei; Silvestre, Martin E; Kirschhöfer, Frank; Brenner-Weiss, Gerald; Franzreb, Matthias

2015-09-11

Porous metal-organic frameworks (MOFs) [Cu3(BTC)2(H2O)3]n (also known as HKUST-1; BTC, benzene-1,3,5-tricarboxylic acid) were synthesized as homogeneous shell onto carboxyl functionalized magnetic microparticles through a liquid phase epitaxy (LPE) process. The as-synthesized core-shell HKUST-1 magnetic microparticles composites were characterized by XRD and SEM, and used as stationary phase in high performance liquid chromatography (HPLC). The effects of the unique properties of MOFs onto the chromatographic performance are demonstrated by the experiments. First, remarkable separation of pyridine and bipyridine is achieved, although both molecules show a strong interaction between the Cu-ions in HKUST-1 and the nitrogen atoms in their heterocyles. The difference can be explained due to size exclusion of bipyridine from the well defined pore structure of crystalline HKUST-1. Second, the enormous variety of possible interactions of sample molecules with the metal ions and linkers within MOFs allows for specifically tailored solid phases for challenging separation tasks. For example, baseline separation of three chloroaniline (CLA) isomers tested can be achieved without the need for gradient elution modes. Along with the experimental HPLC runs, in-depth modelling with a recently developed chromatography modelling software (ChromX) was applied and proofs the software to be a powerful tool for exploring the separation potential of thin MOF films. The pore diffusivity of pyridine and CLA isomers within HKUST-1 are found to be around 2.3×10(-15)m(2)s(-1). While the affinity of HKUST-1 to the tested molecules strongly differs, the maximum capacities are in the same range, with 0.37molL(-1) for pyridine and 0.23molL(-1) for CLA isomers, corresponding to 4.0 and 2.5 molecules per MOF unit cell, respectively. Copyright © 2015 Elsevier B.V. All rights reserved.

Inforna 2.0: A Platform for the Sequence-Based Design of Small Molecules Targeting Structured RNAs.

PubMed

Disney, Matthew D; Winkelsas, Audrey M; Velagapudi, Sai Pradeep; Southern, Mark; Fallahi, Mohammad; Childs-Disney, Jessica L

2016-06-17

The development of small molecules that target RNA is challenging yet, if successful, could advance the development of chemical probes to study RNA function or precision therapeutics to treat RNA-mediated disease. Previously, we described Inforna, an approach that can mine motifs (secondary structures) within target RNAs, which is deduced from the RNA sequence, and compare them to a database of known RNA motif-small molecule binding partners. Output generated by Inforna includes the motif found in both the database and the desired RNA target, lead small molecules for that target, and other related meta-data. Lead small molecules can then be tested for binding and affecting cellular (dys)function. Herein, we describe Inforna 2.0, which incorporates all known RNA motif-small molecule binding partners reported in the scientific literature, a chemical similarity searching feature, and an improved user interface and is freely available via an online web server. By incorporation of interactions identified by other laboratories, the database has been doubled, containing 1936 RNA motif-small molecule interactions, including 244 unique small molecules and 1331 motifs. Interestingly, chemotype analysis of the compounds that bind RNA in the database reveals features in small molecule chemotypes that are privileged for binding. Further, this updated database expanded the number of cellular RNAs to which lead compounds can be identified.

Controlled Bioactive Molecules Delivery Strategies for Tendon and Ligament Tissue Engineering using Polymeric Nanofibers.

PubMed

Hiong Teh, Thomas Kok; Hong Goh, James Cho; Toh, Siew Lok

2015-01-01

The interest in polymeric nanofibers has escalated over the past decade given its promise as tissue engineering scaffolds that can mimic the nanoscale structure of the native extracellular matrix. With functionalization of the polymeric nanofibers using bioactive molecules, localized signaling moieties can be established for the attached cells, to stimulate desired biological effects and direct cellular or tissue response. The inherently high surface area per unit mass of polymeric nanofibers can enhance cell adhesion, bioactive molecules loading and release efficiencies, and mass transfer properties. In this review article, the application of polymeric nanofibers for controlled bioactive molecules delivery will be discussed, with a focus on tendon and ligament tissue engineering. Various polymeric materials of different mechanical and degradation properties will be presented along with the nanofiber fabrication techniques explored. The bioactive molecules of interest for tendon and ligament tissue engineering, including growth factors and small molecules, will also be reviewed and compared in terms of their nanofiber incorporation strategies and release profiles. This article will also highlight and compare various innovative strategies to control the release of bioactive molecules spatiotemporally and explore an emerging tissue engineering strategy involving controlled multiple bioactive molecules sequential release. Finally, the review article concludes with challenges and future trends in the innovation and development of bioactive molecules delivery using polymeric nanofibers for tendon and ligament tissue engineering.

Remote detection of explosives using Raman spectroscopy

NASA Astrophysics Data System (ADS)

Fulton, Jack

2011-05-01

Stand-off detection of potentially hazardous small molecules at distances that allow the user to be safe has many applications, including explosives and chemical threats. The Naval Surface Warfare Center, Crane Division, with EYZtek, Inc. of Ohio, developed a prototype stand-off, eye-safe Raman spectrometer. With a stand-off distance greater than twenty meters and scanning optics, this system has the potential of addressing particularly difficult challenges in small molecule detection. An overview of the system design and desired application space is presented.

Mechanically controllable break junctions for molecular electronics.

PubMed

Xiang, Dong; Jeong, Hyunhak; Lee, Takhee; Mayer, Dirk

2013-09-20

A mechanically controllable break junction (MCBJ) represents a fundamental technique for the investigation of molecular electronic junctions, especially for the study of the electronic properties of single molecules. With unique advantages, the MCBJ technique has provided substantial insight into charge transport processes in molecules. In this review, the techniques for sample fabrication, operation and the various applications of MCBJs are introduced and the history, challenges and future of MCBJs are discussed. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cavity mutants of Savinase. Crystal structures and differential scanning calorimetry experiments give hints of the function of the buried water molecules in subtilisins.

PubMed

Pedersen, J T; Olsen, O H; Betzel, C; Eschenburg, S; Branner, S; Hastrup, S

1994-09-23

The subtilisin molecule possesses several internal water molecules, which may be characterised as an integral part of the protein structure. We have introduced specific mutations (T71I, T71S, T71V, T71A and T71G) at position 71 in the subtilisin variant Savinase from Bacillus lentus. This position is involved in a hydrogen bonded network with several internal water molecules, forming a water channel. The water channel and most of the other internal water molecules are positioned in the interface between two half-domains of the subtilisin molecule. The data presented here indicate that the internal water molecules are structural, and may be the result of trapping during the folding process.

Single molecule junction conductance and binding geometry

NASA Astrophysics Data System (ADS)

Kamenetska, Maria

This Thesis addresses the fundamental problem of controlling transport through a metal-organic interface by studying electronic and mechanical properties of single organic molecule-metal junctions. Using a Scanning Tunneling Microscope (STM) we image, probe energy-level alignment and perform STM-based break junction (BJ) measurements on molecules bound to a gold surface. Using Scanning Tunneling Microscope-based break-junction (STM-BJ) techniques, we explore the effect of binding geometry on single-molecule conductance by varying the structure of the molecules, metal-molecule binding chemistry and by applying sub-nanometer manipulation control to the junction. These experiments are performed both in ambient conditions and in ultra high vacuum (UHV) at cryogenic temperatures. First, using STM imaging and scanning tunneling spectroscopy (STS) measurements we explore binding configurations and electronic properties of an amine-terminated benzene derivative on gold. We find that details of metal-molecule binding affect energy-level alignment at the interface. Next, using the STM-BJ technique, we form and rupture metal-molecule-metal junctions ˜104 times to obtain conductance-vs-extension curves and extract most likely conductance values for each molecule. With these measurements, we demonstrated that the control of junction conductance is possible through a choice of metal-molecule binding chemistry and sub-nanometer positioning. First, we show that molecules terminated with amines, sulfides and phosphines bind selectively on gold and therefore demonstrate constant conductance levels even as the junction is elongated and the metal-molecule attachment point is modified. Such well-defined conductance is also obtained with paracyclophane molecules which bind to gold directly through the pi system. Next, we are able to create metal-molecule-metal junctions with more than one reproducible conductance signatures that can be accessed by changing junction geometry. In the case of pyridine-linked molecules, conductance can be reliably switched between two distinct conductance states using sub-nanometer mechanical manipulation. Using a methyl sulfide linker attached to an oligoene backbone, we are able to create a 3-nm-long molecular potentiometer, whose resistance can be tuned exponentially with Angstom-scale modulations in metal-molecule configuration. These experiments points to a new paradigm for attaining reproducible electrical characteristics of metal-organic devices which involves controlling linker-metal chemistry rather than fabricating identically structured metal-molecule interfaces. By choosing a linker group which is either insensitive to or responds reproducibly to changes in metal-molecule configuration, one can design single molecule devices with functionality more complex than a simple resistor. These ambient temperature experiments were combined with UHV conductance measurements performed in a commercial STM on amine-terminated benzene derivatives which conduct through a non-resonant tunneling mechanism, at temperatures varying from 5 to 300 Kelvin. Our results indicate that while amine-gold binding remains selective irrespective of environment, conductance is not temperature independent, in contrast to what is expected for a tunneling mechanism. Furthermore, using temperature-dependent measurements in ambient conditions we find that HOMO-conducting amines and LUMO-conducting pyridines show opposite dependence of conductance on temperature. These results indicate that energy-level alignment between the molecule and the electrodes changes as a result of varying electrode structure at different temperatures. We find that temperature can serve as a knob with which to tune transport properties of single molecule-metal junctions.

Differences in single and aggregated nanoparticle plasmon spectroscopy.

PubMed

Singh, Pushkar; Deckert-Gaudig, Tanja; Schneidewind, Henrik; Kirsch, Konstantin; van Schrojenstein Lantman, Evelien M; Weckhuysen, Bert M; Deckert, Volker

2015-02-07

Vibrational spectroscopy usually provides structural information averaged over many molecules. We report a larger peak position variation and reproducibly smaller FWHM of TERS spectra compared to SERS spectra indicating that the number of molecules excited in a TERS experiment is extremely low. Thus, orientational averaging effects are suppressed and micro ensembles are investigated. This is shown for a thiophenol molecule adsorbed on Au nanoplates and nanoparticles.

Laser Cooled YbF Molecules for Measuring the Electron's Electric Dipole Moment

NASA Astrophysics Data System (ADS)

Lim, J.; Almond, J. R.; Trigatzis, M. A.; Devlin, J. A.; Fitch, N. J.; Sauer, B. E.; Tarbutt, M. R.; Hinds, E. A.

2018-03-01

We demonstrate one-dimensional sub-Doppler laser cooling of a beam of YbF molecules to 100 μ K . This is a key step towards a measurement of the electron's electric dipole moment using ultracold molecules. We compare the effectiveness of magnetically assisted and polarization-gradient sub-Doppler cooling mechanisms. We model the experiment and find good agreement with our data.

Laser Cooled YbF Molecules for Measuring the Electron's Electric Dipole Moment.

PubMed

Lim, J; Almond, J R; Trigatzis, M A; Devlin, J A; Fitch, N J; Sauer, B E; Tarbutt, M R; Hinds, E A

2018-03-23

We demonstrate one-dimensional sub-Doppler laser cooling of a beam of YbF molecules to 100  μK. This is a key step towards a measurement of the electron's electric dipole moment using ultracold molecules. We compare the effectiveness of magnetically assisted and polarization-gradient sub-Doppler cooling mechanisms. We model the experiment and find good agreement with our data.

Effective diffusion coefficient including the Marangoni effect

NASA Astrophysics Data System (ADS)

Kitahata, Hiroyuki; Yoshinaga, Natsuhiko

2018-04-01

Surface-active molecules supplied from a particle fixed at the water surface create a spatial gradient of the molecule concentration, resulting in Marangoni convection. Convective flow transports the molecules far from the particle, enhancing diffusion. We analytically derive the effective diffusion coefficient associated with the Marangoni convection rolls. The resulting estimated effective diffusion coefficient is consistent with our numerical results and the apparent diffusion coefficient measured in experiments.

Coupled cluster investigation on the thermochemistry of dimethyl sulphide, dimethyl disulphide and their dissociation products: the problem of the enthalpy of formation of atomic sulphur

NASA Astrophysics Data System (ADS)

Denis, Pablo A.

2014-04-01

By means of coupled cluster theory and correlation consistent basis sets we investigated the thermochemistry of dimethyl sulphide (DMS), dimethyl disulphide (DMDS) and four closely related sulphur-containing molecules: CH3SS, CH3S, CH3SH and CH3CH2SH. For the four closed-shell molecules studied, their enthalpies of formation (EOFs) were derived using bomb calorimetry. We found that the deviation of the EOF with respect to experiment was 0.96, 0.65, 1.24 and 1.29 kcal/mol, for CH3SH, CH3CH2SH, DMS and DMDS, respectively, when ΔHf,0 = 65.6 kcal/mol was utilised (JANAF value). However, if the recently proposed ΔHf,0 = 66.2 kcal/mol was used to estimate EOF, the errors dropped to 0.36, 0.05, 0.64 and 0.09 kcal/mol, respectively. In contrast, for the CH3SS radical, a better agreement with experiment was obtained if the 65.6 kcal/mol value was used. To compare with experiment avoiding the problem of the ΔHf,0 (S), we determined the CH3-S and CH3-SS bond dissociation energies (BDEs) in CH3S and CH3SS. At the coupled cluster with singles doubles and perturbative triples correction level of theory, these values are 48.0 and 71.4 kcal/mol, respectively. The latter BDEs are 1.5 and 1.2 kcal/mol larger than the experimental values. The agreement can be considered to be acceptable if we take into consideration that these two radicals present important challenges when determining their EOFs. It is our hope that this work stimulates new studies which help elucidate the problem of the EOF of atomic sulphur.

Model of DNA topology simplification has come full (supercoiled) circle after two decades of research. Comment on "Disentangling DNA molecules" by Alexander Vologodskii

NASA Astrophysics Data System (ADS)

Stasiak, Andrzej

2016-09-01

Being a geek of DNA topology, I remember very well the stir caused by 1997 Science paper showing that DNA topoisomerases have the ability to simplify DNA topology below the topological equilibrium values [1]. In their seminal experiments Rybenkov et al. [1] started with linear double-stranded DNA molecules with cohesive ends. The mutual cohesiveness of DNA ends was due to mutual complementarity of single-stranded extensions at both ends of linear double-stranded DNA molecules. When such DNA molecules were heated up and then slowly cooled down the single-stranded ends eventually annealed with each other causing DNA circularization. This experimental protocol permitted the authors to establish topological/thermodynamic equilibrium within samples of circularized DNA molecules. Among simple unknotted circles one also observed knotted and catenated DNA molecules. The fraction of knotted molecules in DNA samples at topological equilibrium was increasing with the length of DNA molecules undergoing slow circularization. The fraction of catenated molecules was increasing with the length and the concentration of the molecules undergoing slow circularization. Rybenkov et al. incubated then such equilibrated DNA samples with type II DNA topoisomerases, which pass DNA duplex regions through each other, and observed that as the result of it the fraction of knotted and catenated DNA molecules was dramatically decreased (up to 80-fold). This elegant experiment indicated for the first time that type II DNA topoisomerases acting on knotted or catenated DNA molecules have the ability to select among many potential sites of DNA-DNA passages these that result in DNA unknotting or decatenation. Without such a selection topoisomerases could only maintain the original topological equilibrium obtained during the slow cyclization. The big question was how DNA topoisomerases can be directed to do DNA-DNA passages that preferentially result in DNA unknotting and decatenation.

Synthesis of RNA molecules larger than 45 S by isolated rat-liver nucleoli.

PubMed

Grummt, I

1975-09-01

Nucleoli, isolated from rat liver, synthesize in vitro high-molecular-weight RNA, the base composition and sedimentation pattern of which resembles that of ribosomal precursor RNA. In addition, RNA molecules larger than 45 S have been found. In this paper experiments are described which indicate that these large RNA molecules represent geniune transcription products and are not aggregates arising under the experimental conditions employed. This was established by comparing different extraction methods, by sedimentation analysis of the RNA after denaturation with formamide and by pulse-chase experiments. Hybridisation-competition studies showed that 45-S RNA competes with those rapidly molecules to about 80-90%, thus providing evidence for the presence of ribosomal precursor RNA sequences in those long transcription products. Intact nuclei are able to synthesize in the presence of Mg2+ and alpha-amanitin RNA molecules larger than 45 S too, provided that the RNAase activity is suppressed effectively by the addition of cytoplasmic RNAase inhibitor. The significance of these results is discussed with respect to the initial transcript of the rDNA genes in rat liver nucleoli.

Laser mass spectrometry with circularly polarized light: circular dichroism of cold molecules in a supersonic gas beam.

PubMed

Titze, Katharina; Zollitsch, Tilo; Heiz, Ulrich; Boesl, Ulrich

2014-09-15

An experiment on chiral molecules that combines circular dichroism (CD) spectroscopy, mass-selective detection by laser mass spectrometry (MS), and cooling of molecules by using a supersonic beam is presented. The combination of the former two techniques (CD-laser-MS) is a new method to investigate chiral molecules and is now used by several research groups. Cooling in a supersonic beam supplies a substantial increase in spectroscopic resolution, a feature that has not yet been used in CD spectroscopy. In the experiments reported herein, a large variation in the electronic CD of carbonyl 3-methylcyclopentanone was observed depending on the excited vibrational modes in the n → π* transition. This finding should be of interest for the detection of chiral molecules and for the theoretical understanding of the CD of vibronic bands. It is expected that this effect will show up in other chiral carbonyls because the n → π* transition is typical for the carbonyl group. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Influence of hen age on the response of turkey poults to cold stress, Escherichia coli challenge, and treatment with a yeast extract antibiotic alternative.

PubMed

Huff, G R; Huff, W E; Rath, N C; Solis de Los Santos, F; Farnell, M B; Donoghue, A M

2007-04-01

Two battery experiments were conducted to evaluate a commercial yeast extract feed supplement, Alphamune, in a cold stress-Escherichia coli challenge of 1-wk-old turkeys. Experiment 1 used 1-d-old male poults that were the progeny of 33-wk-old hens in their second week of lay. Experiment 2 used male poults of the same genetic line from 40-wk-old hens in their eighth week of lay. Poults were fed a standard unmedicated turkey starter diet or the same diet with either a low level (504 g/t) or a high level (1,008 g/t) of yeast extract. Challenged birds were exposed to intermittent cold stress during wk 1 to 3 and to a respiratory E. coli challenge at 1 wk of age. In both experiments, BW at wk 1 was increased by feeding yeast extract. In experiment 1, challenged, control-fed birds had decreased BW at wk 3 and feed conversion was protected by both levels of yeast extract supplementation. In experiment 2, challenge had no effect on control-fed birds; however, yeast extract decreased the BW of challenged birds. In experiment 1, total leukocyte numbers were decreased by challenge of control-fed birds only, and there was no effect of challenge on the heterophil/lymphocyte ratio. In experiment 2, total leukocyte numbers were decreased and the heterophil/lymphocyte ratio was increased in challenged, control-fed birds. Percentage mortality was not affected by challenge in experiment 1; however, in experiment 2, mortality was increased by challenge of control-fed birds and those fed the lower level of yeast extract. These results suggest that hen age should be considered when designing studies to evaluate antibiotic alternatives and in making decisions for incorporating such alternatives into production.

Programmed Lab Experiments for Biochemical Investigation of Quorum-Sensing Signal Molecules in Rhizospheric Soil Bacteria.

PubMed

Nievas, Fiorela L; Bogino, Pablo C; Giordano, Walter

2016-05-06

Biochemistry courses in the Department of Molecular Biology at the National University of Río Cuarto, Argentina, are designed for undergraduate students in biology, microbiology, chemistry, agronomy, and veterinary medicine. Microbiology students typically have previous coursework in general, analytical, and organic chemistry. Programmed sequences of lab experiments allow these students to investigate biochemical problems whose solution is feasible within the context of their knowledge and experience. We previously designed and reported a programmed lab experiment that familiarizes microbiology students with techniques for detection and characterization of quorum-sensing (QS) and quorum-quenching (QQ) signal molecules. Here, we describe a sequence of experiments designed to expand the understanding and capabilities of biochemistry students using techniques for extraction and identification of QS and QQ signal molecules from peanut rhizospheric soil bacteria, including culturing and manipulation of bacteria under sterile conditions. The program provides students with an opportunity to perform useful assays, draw conclusions from their results, and discuss possible extensions of the study. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:256-262, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

Theory for rates, equilibrium constants, and Brønsted slopes in F1-ATPase single molecule imaging experiments

PubMed Central

Volkán-Kacsó, Sándor; Marcus, Rudolph A.

2015-01-01

A theoretical model of elastically coupled reactions is proposed for single molecule imaging and rotor manipulation experiments on F1-ATPase. Stalling experiments are considered in which rates of individual ligand binding, ligand release, and chemical reaction steps have an exponential dependence on rotor angle. These data are treated in terms of the effect of thermodynamic driving forces on reaction rates, and lead to equations relating rate constants and free energies to the stalling angle. These relations, in turn, are modeled using a formalism originally developed to treat electron and other transfer reactions. During stalling the free energy profile of the enzymatic steps is altered by a work term due to elastic structural twisting. Using biochemical and single molecule data, the dependence of the rate constant and equilibrium constant on the stall angle, as well as the Børnsted slope are predicted and compared with experiment. Reasonable agreement is found with stalling experiments for ATP and GTP binding. The model can be applied to other torque-generating steps of reversible ligand binding, such as ADP and Pi release, when sufficient data become available. PMID:26483483

Single molecule detection with graphene and other two-dimensional materials: nanopores and beyond

PubMed Central

Arjmandi-Tash, Hadi; Belyaeva, Liubov A.

2016-01-01

Graphene and other two dimensional (2D) materials are currently integrated into nanoscaled devices that may – one day – sequence genomes. The challenge to solve is conceptually straightforward: cut a sheet out of a 2D material and use the edge of the sheet to scan an unfolded biomolecule from head to tail. As the scan proceeds – and because 2D materials are atomically thin – the information provided by the edge might be used to identify different segments – ideally single nucleotides – in the biomolecular strand. So far, the most efficient approach was to drill a nano-sized pore in the sheet and use this pore as a channel to guide and detect individual molecules by measuring the electrochemical ionic current. Nanoscaled gaps between two electrodes in 2D materials recently emerged as powerful alternatives to nanopores. This article reviews the current status and prospects of integrating 2D materials in nanopores, nanogaps and similar devices for single molecule biosensing applications. We discuss the pros and cons, the challenges, and the latest achievements in the field. To achieve high-throughput sequencing with 2D materials, interdisciplinary research is essential. PMID:26612268

Caffeine and Sugars Interact in Aqueous Solutions: A Simulation and NMR Study

PubMed Central

Tavagnacco, Letizia; Engström, Olof; Schnupf, Udo; Saboungi, Marie-Louise; Himmel, Michael; Widmalm, Göran; Cesàro, Attilio; Brady, John W.

2012-01-01

Molecular dynamics simulations were carried out on several systems of caffeine interacting with simple sugars. These included a single caffeine molecule in a 3 molal solution of α-D-glucopyranose, at a caffeine concentration of 0.083 molal; a single caffeine in a 3 molal solution of β-D-glucopyranose, and a single caffeine molecule in a 1.08 molal solution of sucrose (table sugar). Parallel Nuclear Magnetic Resonance titration experiments were carried out on the same solutions under similar conditions. Consistent with previous thermodynamic experiments, the sugars were found to have an affinity for the caffeine molecules in both the simulations and experiments, and that the binding in these complexes occurs by face-to-face stacking of the hydrophobic triad of protons of the pyranose rings against the caffeine face, rather than by hydrogen bonding. For the disaccharide, the binding occurs via stacking of the glucose ring against the caffeine, with a lesser affinity for the fructose observed. These findings are consistent with the association being driven by hydrophobic hydration, and are similar to the previously observed binding of glucose rings to various other planar molecules, including indole, serotonin, and phenol. PMID:22897449

Caffeine and sugars interact in aqueous solutions: a simulation and NMR study.

PubMed

Tavagnacco, Letizia; Engström, Olof; Schnupf, Udo; Saboungi, Marie-Louise; Himmel, Michael; Widmalm, Göran; Cesàro, Attilio; Brady, John W

2012-09-27

Molecular dynamics simulations were carried out on several systems of caffeine interacting with simple sugars. These included a single caffeine molecule in a 3 m solution of α-D-glucopyranose, at a caffeine concentration of 0.083 m, a single caffeine in a 3 m solution of β-D-glucopyranose, and a single caffeine molecule in a 1.08 m solution of sucrose (table sugar). Parallel nuclear magnetic resonance titration experiments were carried out on the same solutions under similar conditions. Consistent with previous thermodynamic experiments, the sugars were found to have an affinity for the caffeine molecules in both the simulations and experiments, and the binding in these complexes occurs by face-to-face stacking of the hydrophobic triad of protons of the pyranose rings against the caffeine face, rather than by hydrogen bonding. For the disaccharide, the binding occurs via stacking of the glucose ring against the caffeine, with a lesser affinity for the fructose observed. These findings are consistent with the association being driven by hydrophobic hydration and are similar to the previously observed binding of glucose rings to various other planar molecules, including indole, serotonin, and phenol.

Space flight effects on antioxidant molecules in dry tardigrades: the TARDIKISS experiment.

PubMed

Rizzo, Angela Maria; Altiero, Tiziana; Corsetto, Paola Antonia; Montorfano, Gigliola; Guidetti, Roberto; Rebecchi, Lorena

2015-01-01

The TARDIKISS (Tardigrades in Space) experiment was part of the Biokon in Space (BIOKIS) payload, a set of multidisciplinary experiments performed during the DAMA (Dark Matter) mission organized by Italian Space Agency and Italian Air Force in 2011. This mission supported the execution of experiments in short duration (16 days) taking the advantage of the microgravity environment on board of the Space Shuttle Endeavour (its last mission STS-134) docked to the International Space Station. TARDIKISS was composed of three sample sets: one flight sample and two ground control samples. These samples provided the biological material used to test as space stressors, including microgravity, affected animal survivability, life cycle, DNA integrity, and pathways of molecules working as antioxidants. In this paper we compared the molecular pathways of some antioxidant molecules, thiobarbituric acid reactive substances, and fatty acid composition between flight and control samples in two tardigrade species, namely, Paramacrobiotus richtersi and Ramazzottius oberhaeuseri. In both species, the activities of ROS scavenging enzymes, the total content of glutathione, and the fatty acids composition between flight and control samples showed few significant differences. TARDIKISS experiment, together with a previous space experiment (TARSE), further confirms that both desiccated and hydrated tardigrades represent useful animal tool for space research.

Caging and Photoactivation in Single-Molecule Förster Resonance Energy Transfer Experiments

PubMed Central

2017-01-01

Caged organic fluorophores are established tools for localization-based super-resolution imaging. Their use relies on reversible deactivation of standard organic fluorophores by chemical reduction or commercially available caged dyes with ON switching of the fluorescent signal by ultraviolet (UV) light. Here, we establish caging of cyanine fluorophores and caged rhodamine dyes, i.e., chemical deactivation of fluorescence, for single-molecule Förster resonance energy transfer (smFRET) experiments with freely diffusing molecules. They allow temporal separation and sorting of multiple intramolecular donor–acceptor pairs during solution-based smFRET. We use this “caged FRET” methodology for the study of complex biochemical species such as multisubunit proteins or nucleic acids containing more than two fluorescent labels. Proof-of-principle experiments and a characterization of the uncaging process in the confocal volume are presented. These reveal that chemical caging and UV reactivation allow temporal uncoupling of convoluted fluorescence signals from, e.g., multiple spectrally similar donor or acceptor molecules on nucleic acids. We also use caging without UV reactivation to remove unwanted overlabeled species in experiments with the homotrimeric membrane transporter BetP. We finally outline further possible applications of the caged FRET methodology, such as the study of weak biochemical interactions, which are otherwise impossible with diffusion-based smFRET techniques because of the required low concentrations of fluorescently labeled biomolecules. PMID:28362086

DNA-psoralen interaction: a single molecule experiment.

PubMed

Rocha, M S; Viana, N B; Mesquita, O N

2004-11-15

By attaching one end of a single lambda-DNA molecule to a microscope coverslip and the other end to a polystyrene microsphere trapped by an optical tweezers, we can study the entropic elasticity of the lambda-DNA by measuring force versus extension as we stretch the molecule. This powerful method permits single molecule studies. We are particularly interested in the effects of the photosensitive drug psoralen on the elasticity of the DNA molecule. We have illuminated the sample with different light sources, studying how the different wavelengths affect the psoralen-DNA linkage. To do this, we measure the persistence length of individual DNA-psoralen complexes.

Single Molecule and Collective Dynamics of Motor Protein Coupled with Mechano-Sensitive Chemical Reaction

NASA Astrophysics Data System (ADS)

Iwaki, Mitsuhiro; Marcucci, Lorenzo; Togashi, Yuichi; Yanagida, Toshio

2013-12-01

Motor proteins such as myosin and kinesin hydrolyze ATP into ADP and Pi to convert chemical energy into mechanical work. This resultsin various motile processes like muscle contraction, vesicle transport and cell division. Recent single molecule experiments have revealed that external load applied to these motor proteins perturb not only the mechanical motion, but the ATP hydrolysis cycle as well, making these molecules mechano-enzymes. Here, we describe our single molecule detection techniques to reveal the mechano-enzymatic properties of myosin and introduce recent progress from both experimental and theoretical approaches at the single- and multiple-molecule level.

9 CFR 121.13 - Restricted experiments. 10

Code of Federal Regulations, 2011 CFR

2011-01-01

... publication, “NIH Guidelines for Research Involving Recombinant DNA Molecules.” This document is available on.... (b) Restricted experiments: (1) Experiments utilizing recombinant DNA that involve the deliberate... medicine, or agriculture. (2) Experiments involving the deliberate formation of recombinant DNA containing...

9 CFR 121.13 - Restricted experiments. 10

Code of Federal Regulations, 2010 CFR

2010-01-01

... publication, “NIH Guidelines for Research Involving Recombinant DNA Molecules.” This document is available on.... (b) Restricted experiments: (1) Experiments utilizing recombinant DNA that involve the deliberate... medicine, or agriculture. (2) Experiments involving the deliberate formation of recombinant DNA containing...

9 CFR 121.13 - Restricted experiments. 10

Code of Federal Regulations, 2012 CFR

2012-01-01

... publication, “NIH Guidelines for Research Involving Recombinant DNA Molecules.” This document is available on.... (b) Restricted experiments: (1) Experiments utilizing recombinant DNA that involve the deliberate... medicine, or agriculture. (2) Experiments involving the deliberate formation of recombinant DNA containing...

Pressure-Induced Melting of Confined Ice.

PubMed

Sotthewes, Kai; Bampoulis, Pantelis; Zandvliet, Harold J W; Lohse, Detlef; Poelsema, Bene

2017-12-26

The classic regelation experiment of Thomson in the 1850s deals with cutting an ice cube, followed by refreezing. The cutting was attributed to pressure-induced melting but has been challenged continuously, and only lately consensus emerged by understanding that compression shortens the O:H nonbond and lengthens the H-O bond simultaneously. This H-O elongation leads to energy loss and lowers the melting point. The hot debate survived well over 150 years, mainly due to a poorly defined heat exchange with the environment in the experiment. In our current experiment, we achieved thermal isolation from the environment and studied the fully reversible ice-liquid water transition for water confined between graphene and muscovite mica. We observe a transition from two-dimensional (2D) ice into a quasi-liquid phase by applying a pressure exerted by an atomic force microscopy tip. At room temperature, the critical pressure amounts to about 6 GPa. The transition is completely reversible: refreezing occurs when the applied pressure is lifted. The critical pressure to melt the 2D ice decreases with temperature, and we measured the phase coexistence line between 293 and 333 K. From a Clausius-Clapeyron analysis, we determine the latent heat of fusion of two-dimensional ice at 0.15 eV/molecule, being twice as large as that of bulk ice.

Single Molecule Electronics and Devices

PubMed Central

Tsutsui, Makusu; Taniguchi, Masateru

2012-01-01

The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule. PMID:22969345

Photodissociation of quantum state-selected diatomic molecules yields new insight into ultracold chemistry

NASA Astrophysics Data System (ADS)

McDonald, Mickey; McGuyer, Bart H.; Lee, Chih-Hsi; Apfelbeck, Florian; Zelevinsky, Tanya

2016-05-01

When a molecule is subjected to a sufficiently energetic photon it can break apart into fragments through a process called ``photodissociation''. For over 70 years this simple chemical reaction has served as a vital experimental tool for acquiring information about molecular structure, since the character of the photodissociative transition can be inferred by measuring the 3D photofragment angular distribution (PAD). While theoretical understanding of this process has gradually evolved from classical considerations to a fully quantum approach, experiments to date have not yet revealed the full quantum nature of this process. In my talk I will describe recent experiments involving the photodissociation of ultracold, optical lattice-trapped, and fully quantum state-resolved 88Sr2 molecules. Optical absorption images of the PADs produced in these experiments reveal features which are inherently quantum mechanical in nature, such as matter-wave interference between output channels, and are sensitive to the quantum statistics of the molecular wavefunctions. The results of these experiments cannot be predicted using quasiclassical methods. Instead, we describe our results with a fully quantum mechanical model yielding new intuition about ultracold chemistry.

Organic molecule fluorescence as an experimental test-bed for quantum jumps in thermodynamics

NASA Astrophysics Data System (ADS)

Browne, Cormac; Farrow, Tristan; Dahlsten, Oscar C. O.; Taylor, Robert A.; Vlatko, Vedral

2017-08-01

We demonstrate with an experiment how molecules are a natural test bed for probing fundamental quantum thermodynamics. Single-molecule spectroscopy has undergone transformative change in the past decade with the advent of techniques permitting individual molecules to be distinguished and probed. We demonstrate that the quantum Jarzynski equality for heat is satisfied in this set-up by considering the time-resolved emission spectrum of organic molecules as arising from quantum jumps between states. This relates the heat dissipated into the environment to the free energy difference between the initial and final state. We demonstrate also how utilizing the quantum Jarzynski equality allows for the detection of energy shifts within a molecule, beyond the relative shift.

Organic molecule fluorescence as an experimental test-bed for quantum jumps in thermodynamics.

PubMed

Browne, Cormac; Farrow, Tristan; Dahlsten, Oscar C O; Taylor, Robert A; Vlatko, Vedral

2017-08-01

We demonstrate with an experiment how molecules are a natural test bed for probing fundamental quantum thermodynamics. Single-molecule spectroscopy has undergone transformative change in the past decade with the advent of techniques permitting individual molecules to be distinguished and probed. We demonstrate that the quantum Jarzynski equality for heat is satisfied in this set-up by considering the time-resolved emission spectrum of organic molecules as arising from quantum jumps between states. This relates the heat dissipated into the environment to the free energy difference between the initial and final state. We demonstrate also how utilizing the quantum Jarzynski equality allows for the detection of energy shifts within a molecule, beyond the relative shift.

Activation of Salmonella Typhi-specific regulatory T cells in typhoid disease in a wild-type S. Typhi challenge model.

PubMed

McArthur, Monica A; Fresnay, Stephanie; Magder, Laurence S; Darton, Thomas C; Jones, Claire; Waddington, Claire S; Blohmke, Christoph J; Dougan, Gordon; Angus, Brian; Levine, Myron M; Pollard, Andrew J; Sztein, Marcelo B

2015-05-01

Salmonella Typhi (S. Typhi), the causative agent of typhoid fever, causes significant morbidity and mortality worldwide. Currently available vaccines are moderately efficacious, and identification of immunological responses associated with protection or disease will facilitate the development of improved vaccines. We investigated S. Typhi-specific modulation of activation and homing potential of circulating regulatory T cells (Treg) by flow and mass cytometry using specimens obtained from a human challenge study. Peripheral blood mononuclear cells were obtained from volunteers pre- and at multiple time-points post-challenge with wild-type S. Typhi. We identified differing patterns of S. Typhi-specific modulation of the homing potential of circulating Treg between volunteers diagnosed with typhoid (TD) and those who were not (No TD). TD volunteers demonstrated up-regulation of the gut homing molecule integrin α4ß7 pre-challenge, followed by a significant down-regulation post-challenge consistent with Treg homing to the gut. Additionally, S. Typhi-specific Treg from TD volunteers exhibited up-regulation of activation molecules post-challenge (e.g., HLA-DR, LFA-1). We further demonstrate that depletion of Treg results in increased S. Typhi-specific cytokine production by CD8+ TEM in vitro. These results suggest that the tissue distribution of activated Treg, their characteristics and activation status may play a pivotal role in typhoid fever, possibly through suppression of S. Typhi-specific effector T cell responses. These studies provide important novel insights into the regulation of immune responses that are likely to be critical in protection against typhoid and other enteric infectious diseases.

Electrostatic placement of single ferritin molecules

NASA Astrophysics Data System (ADS)

Kumagai, Shinya; Yoshii, Shigeo; Yamada, Kiyohito; Matsukawa, Nozomu; Fujiwara, Isamu; Iwahori, Kenji; Yamashita, Ichiro

2006-04-01

We electrostatically placed a single ferritin molecule on a nanometric 3-aminopropyltriethoxysilane (APTES) pattern that was on an oxidized Si substrate. The numerical analysis of the total interaction free energy for ferritin predicted that a quadrilateral array of 15nm diameter APTES nanodisks placed at intervals of 100nm would accommodate a single molecule of ferritin in each disk under a Debye length of 14nm. The experiments we conducted conformed to theoretical predictions and we successfully placed a single ferritin molecule on each ATPES disk without ferritin adsorbing on the SiO2 substrate surface.

PHYSICAL FUNDAMENTALS OF QUANTUM ELECTRONICS: Interaction of a sequence of short broad-band radiation pulses with a diatomic molecule

NASA Astrophysics Data System (ADS)

Oraevsky, Anatolii N.; Kozlovskii, Andrei V.; Chichkov, B. N.

1998-07-01

A theoretical analysis is made of the process in which a molecule undergoes a transition between the ground and excited electronic states under the action of a radiation pulse and then, in the interpulse interval, returns to the ground electronic state. Such a periodic process is important in the cooling of molecules by laser radiation. It is shown that the radiation parameters can be selected so that the CO and CN molecules experience over 1000 excitation—relaxation events without dissociation.

Logic Gate Operation by DNA Translocation through Biological Nanopores.

PubMed

Yasuga, Hiroki; Kawano, Ryuji; Takinoue, Masahiro; Tsuji, Yutaro; Osaki, Toshihisa; Kamiya, Koki; Miki, Norihisa; Takeuchi, Shoji

2016-01-01

Logical operations using biological molecules, such as DNA computing or programmable diagnosis using DNA, have recently received attention. Challenges remain with respect to the development of such systems, including label-free output detection and the rapidity of operation. Here, we propose integration of biological nanopores with DNA molecules for development of a logical operating system. We configured outputs "1" and "0" as single-stranded DNA (ssDNA) that is or is not translocated through a nanopore; unlabeled DNA was detected electrically. A negative-AND (NAND) operation was successfully conducted within approximately 10 min, which is rapid compared with previous studies using unlabeled DNA. In addition, this operation was executed in a four-droplet network. DNA molecules and associated information were transferred among droplets via biological nanopores. This system would facilitate linking of molecules and electronic interfaces. Thus, it could be applied to molecular robotics, genetic engineering, and even medical diagnosis and treatment.

Detection of protein-small molecule binding using a self-referencing external cavity laser biosensor.

PubMed

Meng Zhang; Peh, Jessie; Hergenrother, Paul J; Cunningham, Brian T

2014-01-01

High throughput screening of protein-small molecule binding interactions using label-free optical biosensors is challenging, as the detected signals are often similar in magnitude to experimental noise. Here, we describe a novel self-referencing external cavity laser (ECL) biosensor approach that achieves high resolution and high sensitivity, while eliminating thermal noise with sub-picometer wavelength accuracy. Using the self-referencing ECL biosensor, we demonstrate detection of binding between small molecules and a variety of immobilized protein targets with binding affinities or inhibition constants in the sub-nanomolar to low micromolar range. The demonstrated ability to perform detection in the presence of several interfering compounds opens the potential for increasing the throughput of the approach. As an example application, we performed a "needle-in-the-haystack" screen for inhibitors against carbonic anhydrase isozyme II (CA II), in which known inhibitors are clearly differentiated from inactive molecules within a compound library.

Logic Gate Operation by DNA Translocation through Biological Nanopores

PubMed Central

Takinoue, Masahiro; Tsuji, Yutaro; Osaki, Toshihisa; Kamiya, Koki; Miki, Norihisa; Takeuchi, Shoji

2016-01-01

Logical operations using biological molecules, such as DNA computing or programmable diagnosis using DNA, have recently received attention. Challenges remain with respect to the development of such systems, including label-free output detection and the rapidity of operation. Here, we propose integration of biological nanopores with DNA molecules for development of a logical operating system. We configured outputs “1” and “0” as single-stranded DNA (ssDNA) that is or is not translocated through a nanopore; unlabeled DNA was detected electrically. A negative-AND (NAND) operation was successfully conducted within approximately 10 min, which is rapid compared with previous studies using unlabeled DNA. In addition, this operation was executed in a four-droplet network. DNA molecules and associated information were transferred among droplets via biological nanopores. This system would facilitate linking of molecules and electronic interfaces. Thus, it could be applied to molecular robotics, genetic engineering, and even medical diagnosis and treatment. PMID:26890568

A novel porous framework as variable chemo-sensor: from response of specific carcinogenic alkyl-aromatic to selective detection of explosive nitro-aromatics.

PubMed

Chen, Qihui

2018-06-07

Selective probing one molecule from one class similar molecules is highly challenging due to their similar chemical and physical properties. Here, a novel metal-organic framework FJI-H15 with flexible porous cages has been designed and synthesized, which can specifically recognize ethyl-benzene with ultrahigh enhancement efficiency from series of alkyl-aromatics, in which an unusual size-dependent interaction has been found and proved. While it also can selectively detect phenolic-nitroaromatics among series of nitro-aromatics based on energy transferring and electrostatic interaction. Such unusual specificity and variable mechanisms responding to different type molecules has not been reported, which will provide a new strategy for developing more effective chemo-sensor based on MOFs for probing small structural differences in molecules. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Aligned 1-D nanorods of a π-gelator exhibit molecular orientation and excitation energy transport different from entangled fiber networks.

PubMed

Sakakibara, Keita; Chithra, Parayalil; Das, Bidisa; Mori, Taizo; Akada, Misaho; Labuta, Jan; Tsuruoka, Tohru; Maji, Subrata; Furumi, Seiichi; Shrestha, Lok Kumar; Hill, Jonathan P; Acharya, Somobrata; Ariga, Katsuhiko; Ajayaghosh, Ayyappanpillai

2014-06-18

Linear π-gelators self-assemble into entangled fibers in which the molecules are arranged perpendicular to the fiber long axis. However, orientation of gelator molecules in a direction parallel to the long axes of the one-dimensional (1-D) structures remains challenging. Herein we demonstrate that, at the air-water interface, an oligo(p-phenylenevinylene)-derived π-gelator forms aligned nanorods of 340 ± 120 nm length and 34 ± 5 nm width, in which the gelator molecules are reoriented parallel to the long axis of the rods. The orientation change of the molecules results in distinct excited-state properties upon local photoexcitation, as evidenced by near-field scanning optical microscopy. A detailed understanding of the mechanism by which excitation energy migrates through these 1-D molecular assemblies might help in the design of supramolecular structures with improved charge-transport properties.

Search for complex organic molecules in space

NASA Astrophysics Data System (ADS)

Ohishi, Masatoshi

2016-07-01

It was 1969 when the first organic molecule in space, H2CO, was discovered. Since then many organic molecules were discovered by using the NRAO 11 m (upgraded later to 12 m), Nobeyama 45 m, IRAM 30 m, and other highly sensitive radio telescopes as a result of close collaboration between radio astronomers and microwave spectroscopists. It is noteworthy that many famous organic molecules such as CH3OH, C2H5OH, (CH3)2O and CH3NH2 were detected by 1975. Organic molecules were found in so-called hot cores where molecules were thought to form on cold dust surfaces and then to evaporate by the UV photons emitted from the central star. These days organic molecules are known to exist not only in hot cores but in hot corinos (a warm, compact molecular clump found in the inner envelope of a class 0 protostar) and even protoplanetary disks. As was described above, major organic molecules were known since 1970s. It was very natural that astronomers considered a relationship between organic molecules in space and the origin of life. Several astronomers challenged to detect glycine and other prebiotic molecules without success. ALMA is expected to detect such important materials to further consider the gexogenous deliveryh hypothesis. In this paper I summarize the history in searching for complex organic molecules together with difficulties in observing very weak signals from larger species. The awfully long list of references at the end of this article may be the most useful part for readers who want to feel the exciting discovery stories.

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

Lykkebo, Jacob; Solomon, Gemma C., E-mail: gsolomon@nano.ku.dk; Romano, Giuseppe

Electronic devices composed of single molecules constitute the ultimate limit in the continued downscaling of electronic components. A key challenge for single-molecule electronics is to control the temperature of these junctions. Controlling heating and cooling effects in individual vibrational modes can, in principle, be utilized to increase stability of single-molecule junctions under bias, to pump energy into particular vibrational modes to perform current-induced reactions, or to increase the resolution in inelastic electron tunneling spectroscopy by controlling the life-times of phonons in a molecule by suppressing absorption and external dissipation processes. Under bias the current and the molecule exchange energy, whichmore » typically results in heating of the molecule. However, the opposite process is also possible, where energy is extracted from the molecule by the tunneling current. Designing a molecular “heat sink” where a particular vibrational mode funnels heat out of the molecule and into the leads would be very desirable. It is even possible to imagine how the vibrational energy of the other vibrational modes could be funneled into the “cooling mode,” given the right molecular design. Previous efforts to understand heating and cooling mechanisms in single molecule junctions have primarily been concerned with small models, where it is unclear which molecular systems they correspond to. In this paper, our focus is on suppressing heating and obtaining current-induced cooling in certain vibrational modes. Strategies for cooling vibrational modes in single-molecule junctions are presented, together with atomistic calculations based on those strategies. Cooling and reduced heating are observed for two different cooling schemes in calculations of atomistic single-molecule junctions.« less

Toward the laboratory identification of the not-so-simple NS2 neutral and anion isomers

NASA Astrophysics Data System (ADS)

Fortenberry, Ryan C.; Thackston, Russell; Francisco, Joseph S.; Lee, Timothy J.

2017-08-01

The NS2 radical is a simple arrangement of atoms with a complex electronic structure. This molecule was first reported by Hassanzadeh and Andrew's group [J. Am. Chem. Soc. 114, 83 (1992)] through Ar matrix isolation experiments. In the quarter century since this seminal work was published, almost nothing has been reported about nitrogen disulfide even though NS2 is isovalent with the common NO2. The present study aims to shed new insight into possible challenges with the characterization of this radical. No less than three potential energy surfaces all intersect in the C2v region of the SNS radical isomer. A type-C Renner-Teller molecule is present for the linear 2Πu state where the potential energy surface is fully contained within the 2.05 kcal/mol lower energy X ˜ 2A1 state. A C2v, 1 2B1 state is present in this same region, but a double excitation is required to access this state from the X ˜ 2A1 state of SNS. Additionally, a 1 2A' NSS isomer is also present but with notable differences in the geometry from the global minimum. Consequently, the rovibronic spectrum of these NS2 isomers is quite complicated. While the present theory and previous Ar matrix experiments agree well on isotopic shifts, they differ notably for the absolute fundamental vibrational frequency transitions. These differences are likely a combination of matrix shifts and issues associated with the neglect of non-adiabatic coupling in the computations. In either case, it is clear that high-resolution gas phase experimental observations will be complicated to sort. The present computations should aid in their analysis.

A Magic-Angle Spinning NMR Method for the Site-Specific Measurement of Proton Chemical-Shift Anisotropy in Biological and Organic Solids.

PubMed

Hou, Guangjin; Gupta, Rupal; Polenova, Tatyana; Vega, Alexander J

2014-02-01

Proton chemical shifts are a rich probe of structure and hydrogen bonding environments in organic and biological molecules. Until recently, measurements of 1 H chemical shift tensors have been restricted to either solid systems with sparse proton sites or were based on the indirect determination of anisotropic tensor components from cross-relaxation and liquid-crystal experiments. We have introduced an MAS approach that permits site-resolved determination of CSA tensors of protons forming chemical bonds with labeled spin-1/2 nuclei in fully protonated solids with multiple sites, including organic molecules and proteins. This approach, originally introduced for the measurements of chemical shift tensors of amide protons, is based on three RN -symmetry based experiments, from which the principal components of the 1 H CS tensor can be reliably extracted by simultaneous triple fit of the data. In this article, we expand our approach to a much more challenging system involving aliphatic and aromatic protons. We start with a review of the prior work on experimental-NMR and computational-quantum-chemical approaches for the measurements of 1 H chemical shift tensors and for relating these to the electronic structures. We then present our experimental results on U- 13 C, 15 N-labeled histdine demonstrating that 1 H chemical shift tensors can be reliably determined for the 1 H 15 N and 1 H 13 C spin pairs in cationic and neutral forms of histidine. Finally, we demonstrate that the experimental 1 H(C) and 1 H(N) chemical shift tensors are in agreement with Density Functional Theory calculations, therefore establishing the usefulness of our method for characterization of structure and hydrogen bonding environment in organic and biological solids.

Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions.

PubMed

Götz, Markus; Wortmann, Philipp; Schmid, Sonja; Hugel, Thorsten

2018-01-30

Single-molecule Förster resonance energy transfer (smFRET) has become a widely used biophysical technique to study the dynamics of biomolecules. For many molecular machines in a cell proteins have to act together with interaction partners in a functional cycle to fulfill their task. The extension of two-color to multi-color smFRET makes it possible to simultaneously probe more than one interaction or conformational change. This not only adds a new dimension to smFRET experiments but it also offers the unique possibility to directly study the sequence of events and to detect correlated interactions when using an immobilized sample and a total internal reflection fluorescence microscope (TIRFM). Therefore, multi-color smFRET is a versatile tool for studying biomolecular complexes in a quantitative manner and in a previously unachievable detail. Here, we demonstrate how to overcome the special challenges of multi-color smFRET experiments on proteins. We present detailed protocols for obtaining the data and for extracting kinetic information. This includes trace selection criteria, state separation, and the recovery of state trajectories from the noisy data using a 3D ensemble Hidden Markov Model (HMM). Compared to other methods, the kinetic information is not recovered from dwell time histograms but directly from the HMM. The maximum likelihood framework allows us to critically evaluate the kinetic model and to provide meaningful uncertainties for the rates. By applying our method to the heat shock protein 90 (Hsp90), we are able to disentangle the nucleotide binding and the global conformational changes of the protein. This allows us to directly observe the cooperativity between the two nucleotide binding pockets of the Hsp90 dimer.

Improved Prediction of Bovine Leucocyte Antigens (BoLA) Presented Ligands by Use of Mass-Spectrometry-Determined Ligand and in Vitro Binding Data

PubMed Central

2017-01-01

Peptide binding to MHC class I molecules is the single most selective step in antigen presentation and the strongest single correlate to peptide cellular immunogenicity. The cost of experimentally characterizing the rules of peptide presentation for a given MHC-I molecule is extensive, and predictors of peptide–MHC interactions constitute an attractive alternative. Recently, an increasing amount of MHC presented peptides identified by mass spectrometry (MS ligands) has been published. Handling and interpretation of MS ligand data is, in general, challenging due to the polyspecificity nature of the data. We here outline a general pipeline for dealing with this challenge and accurately annotate ligands to the relevant MHC-I molecule they were eluted from by use of GibbsClustering and binding motif information inferred from in silico models. We illustrate the approach here in the context of MHC-I molecules (BoLA) of cattle. Next, we demonstrate how such annotated BoLA MS ligand data can readily be integrated with in vitro binding affinity data in a prediction model with very high and unprecedented performance for identification of BoLA-I restricted T-cell epitopes. The prediction model is freely available at http://www.cbs.dtu.dk/services/NetMHCpan/NetBoLApan. The approach has here been applied to the BoLA-I system, but the pipeline is readily applicable to MHC systems in other species. PMID:29115832

Improved Prediction of Bovine Leucocyte Antigens (BoLA) Presented Ligands by Use of Mass-Spectrometry-Determined Ligand and in Vitro Binding Data.

PubMed

Nielsen, Morten; Connelley, Tim; Ternette, Nicola

2018-01-05

Peptide binding to MHC class I molecules is the single most selective step in antigen presentation and the strongest single correlate to peptide cellular immunogenicity. The cost of experimentally characterizing the rules of peptide presentation for a given MHC-I molecule is extensive, and predictors of peptide-MHC interactions constitute an attractive alternative. Recently, an increasing amount of MHC presented peptides identified by mass spectrometry (MS ligands) has been published. Handling and interpretation of MS ligand data is, in general, challenging due to the polyspecificity nature of the data. We here outline a general pipeline for dealing with this challenge and accurately annotate ligands to the relevant MHC-I molecule they were eluted from by use of GibbsClustering and binding motif information inferred from in silico models. We illustrate the approach here in the context of MHC-I molecules (BoLA) of cattle. Next, we demonstrate how such annotated BoLA MS ligand data can readily be integrated with in vitro binding affinity data in a prediction model with very high and unprecedented performance for identification of BoLA-I restricted T-cell epitopes. The prediction model is freely available at http://www.cbs.dtu.dk/services/NetMHCpan/NetBoLApan . The approach has here been applied to the BoLA-I system, but the pipeline is readily applicable to MHC systems in other species.

Intelligent chiral sensing based on supramolecular and interfacial concepts.

PubMed

Ariga, Katsuhiko; Richards, Gary J; Ishihara, Shinsuke; Izawa, Hironori; Hill, Jonathan P

2010-01-01

Of the known intelligently-operating systems, the majority can undoubtedly be classed as being of biological origin. One of the notable differences between biological and artificial systems is the important fact that biological materials consist mostly of chiral molecules. While most biochemical processes routinely discriminate chiral molecules, differentiation between chiral molecules in artificial systems is currently one of the challenging subjects in the field of molecular recognition. Therefore, one of the important challenges for intelligent man-made sensors is to prepare a sensing system that can discriminate chiral molecules. Because intermolecular interactions and detection at surfaces are respectively parts of supramolecular chemistry and interfacial science, chiral sensing based on supramolecular and interfacial concepts is a significant topic. In this review, we briefly summarize recent advances in these fields, including supramolecular hosts for color detection on chiral sensing, indicator-displacement assays, kinetic resolution in supramolecular reactions with analyses by mass spectrometry, use of chiral shape-defined polymers, such as dynamic helical polymers, molecular imprinting, thin films on surfaces of devices such as QCM, functional electrodes, FET, and SPR, the combined technique of magnetic resonance imaging and immunoassay, and chiral detection using scanning tunneling microscopy and cantilever technology. In addition, we will discuss novel concepts in recent research including the use of achiral reagents for chiral sensing with NMR, and mechanical control of chiral sensing. The importance of integration of chiral sensing systems with rapidly developing nanotechnology and nanomaterials is also emphasized.

Applying Superresolution Localization-Based Microscopy to Neurons

PubMed Central

ZHONG, HAINING

2016-01-01

Proper brain function requires the precise localization of proteins and signaling molecules on a nanometer scale. The examination of molecular organization at this scale has been difficult in part because it is beyond the reach of conventional, diffraction-limited light microscopy. The recently developed method of superresolution, localization-based fluorescent microscopy (LBM), such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), has demonstrated a resolving power at a 10 nm scale and is poised to become a vital tool in modern neuroscience research. Indeed, LBM has revealed previously unknown cellular architectures and organizational principles in neurons. Here, we discuss the principles of LBM, its current applications in neuroscience, and the challenges that must be met before its full potential is achieved. We also present the unpublished results of our own experiments to establish a sample preparation procedure for applying LBM to study brain tissue. PMID:25648102

Regulatory and clinical considerations for biosimilar oncology drugs

PubMed Central

Bennett, Charles L; Chen, Brian; Hermanson, Terhi; Wyatt, Michael D; Schulz, Richard M; Georgantopoulos, Peter; Kessler, Samuel; Raisch, Dennis W; Qureshi, Zaina P; Lu, Z Kevin; Love, Bryan L; Noxon, Virginia; Bobolts, Laura; Armitage, Melissa; Bian, John; Ray, Paul; Ablin, Richard J; Hrushesky, William J; Macdougall, Iain C; Sartor, Oliver; Armitage, James O

2015-01-01

Biological oncology products are integral to cancer treatment, but their high costs pose challenges to patients, families, providers, and insurers. The introduction of biosimilar agents—molecules that are similar in structure, function, activity, immunogenicity, and safety to the original biological drugs—provide opportunities both to improve healthcare access and outcomes, and to reduce costs. Several international regulatory pathways have been developed to expedite entry of biosimilars into global marketplaces. The first wave of oncology biosimilar use was in Europe and India in 2007. Oncology biosimilars are now widely marketed in several countries in Europe, and in Australia, Japan, China, Russia, India, and South Korea. Their use is emerging worldwide, with the notable exception of the USA, where several regulatory and cost barriers to biosimilar approval exist. In this Review, we discuss oncology biosimilars and summarise their regulatory frameworks, clinical experiences, and safety concerns. PMID:25456378

Using simple manipulatives to improve student comprehension of a complex biological process: protein synthesis.

PubMed

Guzman, Karen; Bartlett, John

2012-01-01

Biological systems and living processes involve a complex interplay of biochemicals and macromolecular structures that can be challenging for undergraduate students to comprehend and, thus, misconceptions abound. Protein synthesis, or translation, is an example of a biological process for which students often hold many misconceptions. This article describes an exercise that was developed to illustrate the process of translation using simple objects to represent complex molecules. Animations, 3D physical models, computer simulations, laboratory experiments and classroom lectures are also used to reinforce the students' understanding of translation, but by focusing on the simple manipulatives in this exercise, students are better able to visualize concepts that can elude them when using the other methods. The translation exercise is described along with suggestions for background material, questions used to evaluate student comprehension and tips for using the manipulatives to identify common misconceptions. Copyright © 2012 Wiley Periodicals, Inc.

Twelve-fold increase in the number of usable ThO molecules for the ACME electron electric dipole measurement through STIRAP

NASA Astrophysics Data System (ADS)

Panda, C. D.; O'Leary, B. R.; Lasner, Z.; Petrik, E. S.; West, A. D.; Demille, D.; Doyle, J. M.; Gabrielse, G.

2016-05-01

The ACME Collaboration recently reported an order of magnitude improved limit on the electric dipole moment of the electron (eEDM), setting more stringent constraints on many time reversal (T) violating extensions to the Standard Model. The experiment was performed using spin precession measurements in a molecular beam of thorium oxide. We report here on a new method of preparing the coherent spin superposition state that serves as the initial state of the spin precession measurement using STImulated Raman Adiabatic Passage (STIRAP). We demonstrate a transfer efficiency of 75 % , giving a twelve-fold increase in signal. We discuss the particularities of implementing STIRAP in the ACME measurement and the methods we have used to overcome various challenges. This work was performed as part of the ACME Collaboration, to whom we are grateful for its contributions, and was supported by the NSF.

Force-detected nanoscale absorption spectroscopy in water at room temperature using an optical trap

NASA Astrophysics Data System (ADS)

Parobek, Alexander; Black, Jacob W.; Kamenetska, Maria; Ganim, Ziad

2018-04-01

Measuring absorption spectra of single molecules presents a fundamental challenge for standard transmission-based instruments because of the inherently low signal relative to the large background of the excitation source. Here we demonstrate a new approach for performing absorption spectroscopy in solution using a force measurement to read out optical excitation at the nanoscale. The photoinduced force between model chromophores and an optically trapped gold nanoshell has been measured in water at room temperature. This photoinduced force is characterized as a function of wavelength to yield the force spectrum, which is shown to be correlated to the absorption spectrum for four model systems. The instrument constructed for these measurements combines an optical tweezer with frequency domain absorption spectroscopy over the 400-800 nm range. These measurements provide proof-of-principle experiments for force-detected nanoscale spectroscopies that operate under ambient chemical conditions.

Force feedback effects on single molecule hopping and pulling experiments

NASA Astrophysics Data System (ADS)

Rico-Pasto, M.; Pastor, I.; Ritort, F.

2018-03-01

Single-molecule experiments with optical tweezers have become an important tool to study the properties and mechanisms of biological systems, such as cells and nucleic acids. In particular, force unzipping experiments have been used to extract the thermodynamics and kinetics of folding and unfolding reactions. In hopping experiments, a molecule executes transitions between the unfolded and folded states at a preset value of the force [constant force mode (CFM) under force feedback] or trap position [passive mode (PM) without feedback] and the force-dependent kinetic rates extracted from the lifetime of each state (CFM) and the rupture force distributions (PM) using the Bell-Evans model. However, hopping experiments in the CFM are known to overestimate molecular distances and folding free energies for fast transitions compared to the response time of the feedback. In contrast, kinetic rate measurements from pulling experiments have been mostly done in the PM while the CFM is seldom implemented in pulling protocols. Here, we carry out hopping and pulling experiments in a short DNA hairpin in the PM and CFM at three different temperatures (6 °C, 25 °C, and 45 °C) exhibiting largely varying kinetic rates. As expected, we find that equilibrium hopping experiments in the CFM and PM perform well at 6 °C (where kinetics are slow), whereas the CFM overestimates molecular parameters at 45 °C (where kinetics are fast). In contrast, nonequilibrium pulling experiments perform well in both modes at all temperatures. This demonstrates that the same kind of feedback algorithm in the CFM leads to more reliable determination of the folding reaction parameters in irreversible pulling experiments.

Force feedback effects on single molecule hopping and pulling experiments.

PubMed

Rico-Pasto, M; Pastor, I; Ritort, F

2018-03-28

Single-molecule experiments with optical tweezers have become an important tool to study the properties and mechanisms of biological systems, such as cells and nucleic acids. In particular, force unzipping experiments have been used to extract the thermodynamics and kinetics of folding and unfolding reactions. In hopping experiments, a molecule executes transitions between the unfolded and folded states at a preset value of the force [constant force mode (CFM) under force feedback] or trap position [passive mode (PM) without feedback] and the force-dependent kinetic rates extracted from the lifetime of each state (CFM) and the rupture force distributions (PM) using the Bell-Evans model. However, hopping experiments in the CFM are known to overestimate molecular distances and folding free energies for fast transitions compared to the response time of the feedback. In contrast, kinetic rate measurements from pulling experiments have been mostly done in the PM while the CFM is seldom implemented in pulling protocols. Here, we carry out hopping and pulling experiments in a short DNA hairpin in the PM and CFM at three different temperatures (6 °C, 25 °C, and 45 °C) exhibiting largely varying kinetic rates. As expected, we find that equilibrium hopping experiments in the CFM and PM perform well at 6 °C (where kinetics are slow), whereas the CFM overestimates molecular parameters at 45 °C (where kinetics are fast). In contrast, nonequilibrium pulling experiments perform well in both modes at all temperatures. This demonstrates that the same kind of feedback algorithm in the CFM leads to more reliable determination of the folding reaction parameters in irreversible pulling experiments.

Recent patents of nanopore DNA sequencing technology: progress and challenges.

PubMed

Zhou, Jianfeng; Xu, Bingqian

2010-11-01

DNA sequencing techniques witnessed fast development in the last decades, primarily driven by the Human Genome Project. Among the proposed new techniques, Nanopore was considered as a suitable candidate for the single DNA sequencing with ultrahigh speed and very low cost. Several fabrication and modification techniques have been developed to produce robust and well-defined nanopore devices. Many efforts have also been done to apply nanopore to analyze the properties of DNA molecules. By comparing with traditional sequencing techniques, nanopore has demonstrated its distinctive superiorities in main practical issues, such as sample preparation, sequencing speed, cost-effective and read-length. Although challenges still remain, recent researches in improving the capabilities of nanopore have shed a light to achieve its ultimate goal: Sequence individual DNA strand at single nucleotide level. This patent review briefly highlights recent developments and technological achievements for DNA analysis and sequencing at single molecule level, focusing on nanopore based methods.

Small-scale Detonation Velocity Measurement of Select CL-20 Cocrystals

NASA Astrophysics Data System (ADS)

Vuppuluri, Vasant; Gunduz, I. Emre; Son, Steven F.

2017-06-01

The challenge of developing novel energetic materials makes cocrystallization using existing energetic molecules useful. Cocrystallization of CL-20 with other high explosives such as HMX has been demonstrated previously to yield novel energetic materials and may have favorable detonation performance. However, detonation performance characterization of these cocrystals is challenging due to limited availability of material. Also, the contribution of bonding energy between coformers contained within the cocrystal is not well-understood. We present the comparison of steady detonation velocities of CL-20 cocrystals to their corresponding physical mixtures using microwave interferometry. With less than 1.5 g of the cocrystal material contained within 6.52 mm diameter charges, shot-to-shot variation in detonation velocity of only about 100 m/s are achievable with this technique. This variation is adequate to resolve relatively small differences between physical mixed explosive molecules and cocrystals.

Non-equilibrium assembly of microtubules: from molecules to autonomous chemical robots.

PubMed

Hess, H; Ross, Jennifer L

2017-09-18

Biological systems have evolved to harness non-equilibrium processes from the molecular to the macro scale. It is currently a grand challenge of chemistry, materials science, and engineering to understand and mimic biological systems that have the ability to autonomously sense stimuli, process these inputs, and respond by performing mechanical work. New chemical systems are responding to the challenge and form the basis for future responsive, adaptive, and active materials. In this article, we describe a particular biochemical-biomechanical network based on the microtubule cytoskeletal filament - itself a non-equilibrium chemical system. We trace the non-equilibrium aspects of the system from molecules to networks and describe how the cell uses this system to perform active work in essential processes. Finally, we discuss how microtubule-based engineered systems can serve as testbeds for autonomous chemical robots composed of biological and synthetic components.

Evaluating the potential energy landscape over single molecules at room temperature with lateral force microscopy

NASA Astrophysics Data System (ADS)

Weymouth, Alfred J.; Riegel, Elisabeth; Matencio, Sonia; Giessibl, Franz J.

2018-04-01

One of the challenges of AFM, in contrast to STM, is that the measured signal includes both long-range and short-range components. The most accurate method for removing long-range components is to measure both on and off an adsorbate and to subtract the difference. This on-off method is challenging at room temperature due to thermal drift. By moving to a non-contact scheme in which the lateral component of the force interaction is probed, the measurement is dominated by short-range interactions. We use frequency-modulation lateral force microscopy to measure individual PTCDA molecules adsorbed on Ag/Si(111)-( √{3 }×√{3 } ). By fitting the data to a model potential, we can extract the depth and width of the potential. When the tip is closer to the sample, a repulsive feature can be observed in the data.

Virtual Screening with AutoDock: Theory and Practice

PubMed Central

Cosconati, Sandro; Forli, Stefano; Perryman, Alex L.; Harris, Rodney; Goodsell, David S.; Olson, Arthur J.

2011-01-01

Importance to the field Virtual screening is a computer-based technique for identifying promising compounds to bind to a target molecule of known structure. Given the rapidly increasing number of protein and nucleic acid structures, virtual screening continues to grow as an effective method for the discovery of new inhibitors and drug molecules. Areas covered in this review We describe virtual screening methods that are available in the AutoDock suite of programs, and several of our successes in using AutoDock virtual screening in pharmaceutical lead discovery. What the reader will gain A general overview of the challenges of virtual screening is presented, along with the tools available in the AutoDock suite of programs for addressing these challenges. Take home message Virtual screening is an effective tool for the discovery of compounds for use as leads in drug discovery, and the free, open source program AutoDock is an effective tool for virtual screening. PMID:21532931

Single molecule photobleaching (SMPB) technology for counting of RNA, DNA, protein and other molecules in nanoparticles and biological complexes by TIRF instrumentation.

PubMed

Zhang, Hui; Guo, Peixuan

2014-05-15

Direct counting of biomolecules within biological complexes or nanomachines is demanding. Single molecule counting using optical microscopy is challenging due to the diffraction limit. The single molecule photobleaching (SMPB) technology for direct counting developed by our team (Shu et al., 2007 [18]; Zhang et al., 2007 [19]) offers a simple and straightforward method to determine the stoichiometry of molecules or subunits within biocomplexes or nanomachines at nanometer scales. Stoichiometry is determined by real-time observation of the number of descending steps resulted from the photobleaching of individual fluorophore. This technology has now been used extensively for single molecule counting of protein, RNA, and other macromolecules in a variety of complexes or nanostructures. Here, we elucidate the SMPB technology, using the counting of RNA molecules within a bacteriophage phi29 DNA-packaging biomotor as an example. The method described here can be applied to the single molecule counting of other molecules in other systems. The construction of a concise, simple and economical single molecule total internal reflection fluorescence (TIRF) microscope combining prism-type and objective-type TIRF is described. The imaging system contains a deep-cooled sensitive EMCCD camera with single fluorophore detection sensitivity, a laser combiner for simultaneous dual-color excitation, and a Dual-View™ imager to split the multiple outcome signals to different detector channels based on their wavelengths. Methodology of the single molecule photobleaching assay used to elucidate the stoichiometry of RNA on phi29 DNA packaging motor and the mechanism of protein/RNA interaction are described. Different methods for single fluorophore labeling of RNA molecules are reviewed. The process of statistical modeling to reveal the true copy number of the biomolecules based on binomial distribution is also described. Copyright © 2014 Elsevier Inc. All rights reserved.

Imaging the cell surface and its organization down to the level of single molecules.

PubMed

Klenerman, David; Shevchuk, Andrew; Novak, Pavel; Korchev, Yuri E; Davis, Simon J

2013-02-05

Determining the organization of key molecules on the surface of live cells in two dimensions and how this changes during biological processes, such as signalling, is a major challenge in cell biology and requires methods with nanoscale spatial resolution and high temporal resolution. Here, we review biophysical tools, based on scanning ion conductance microscopy and single-molecule fluorescence and the combination of both of these methods, which have recently been developed to address these issues. We then give examples of how these methods have been be applied to provide new insights into cell membrane organization and function, and discuss some of the issues that will need to be addressed to further exploit these methods in the future.

Can formulation and drug delivery reduce attrition during drug discovery and development—review of feasibility, benefits and challenges

PubMed Central

Basavaraj, S; Betageri, Guru V.

2014-01-01

Drug discovery and development has become longer and costlier process. The fear of failure and stringent regulatory review process is driving pharmaceutical companies towards “me too” drugs and improved generics (505(b) (2)) fillings. The discontinuance of molecules at late stage clinical trials is common these years. The molecules are withdrawn at various stages of discovery and development process for reasons such as poor ADME properties, lack of efficacy and safety reasons. Hence this review focuses on possible applications of formulation and drug delivery to salvage molecules and improve the drugability. The formulation and drug delivery technologies are suitable for addressing various issues contributing to attrition are discussed in detail. PMID:26579359

Single molecule experimentation in biological physics: exploring the living component of soft condensed matter one molecule at a time.

PubMed

Harriman, O L J; Leake, M C

2011-12-21

The soft matter of biological systems consists of mesoscopic length scale building blocks, composed of a variety of different types of biological molecules. Most single biological molecules are so small that 1 billion would fit on the full-stop at the end of this sentence, but collectively they carry out the vital activities in living cells whose length scale is at least three orders of magnitude greater. Typically, the number of molecules involved in any given cellular process at any one time is relatively small, and so real physiological events may often be dominated by stochastics and fluctuation behaviour at levels comparable to thermal noise, and are generally heterogeneous in nature. This challenging combination of heterogeneity and stochasticity is best investigated experimentally at the level of single molecules, as opposed to more conventional bulk ensemble-average techniques. In recent years, the use of such molecular experimental approaches has become significantly more widespread in research laboratories around the world. In this review we discuss recent experimental approaches in biological physics which can be applied to investigate the living component of soft condensed matter to a precision of a single molecule. © 2011 IOP Publishing Ltd Printed in the UK & the USA

Chirality-sensitive microwave spectroscopy - application to terpene molecules

NASA Astrophysics Data System (ADS)

Schnell, Melanie

Most molecules of biochemical relevance are chiral. Even though the physical properties of two enantiomers are nearly identical, they might exhibit completely different biochemical effects, such as different odor in the case of carvone. In nature and as products of chemical syntheses, chiral molecules often exist in mixtures with other chiral molecules. The analysis of these complex mixtures to identify the molecular components, to determine which enantiomers are present, and to measure the enantiomeric excesses (ee) is still one of the challenging and very important tasks of analytical chemistry. We recently experimentally demonstrated a new method of differentiating enantiomeric pairs of chiral molecules in the gas phase. It is based on broadband rotational spectroscopy and is a three-wave mixing process that involves a closed cycle of three rotational transitions. The phase of the acquired signal bares the signature of the enantiomer, as it depends upon the product of the transition dipole moments. Furthermore, because the signal amplitude is proportional to the ee, this technique allows not only for determining which enantiomer is in excess, but also by how much. A unique advantage of our technique is that it can also be applied to mixtures of chiral molecules, even when the molecules are very similar. In my lecture, I will introduce the technique and give an update on the recent developments.

Development of novel vaccines using DNA shuffling and screening strategies.

PubMed

Locher, Christopher P; Soong, Nay Wei; Whalen, Robert G; Punnonen, Juha

2004-02-01

DNA shuffling and screening technologies recombine and evolve genes in vitro to rapidly obtain molecules with improved biological activity and fitness. In this way, genes from related strains are bred like plants or livestock and their successive progeny are selected. These technologies have also been called molecular breeding-directed molecular evolution. Recent developments in bioinformatics-assisted computer programs have facilitated the design, synthesis and analysis of DNA shuffled libraries of chimeric molecules. New applications in vaccine development are among the key features of DNA shuffling and screening technologies because genes from several strains or antigenic variants of pathogens can be recombined to create novel molecules capable of inducing immune responses that protect against infections by multiple strains of pathogens. In addition, molecules such as co-stimulatory molecules and cytokines have been evolved to have improved T-cell proliferation and cytokine production compared with the wild-type human molecules. These molecules can be used to immunomodulate vaccine responsiveness and have multiple applications in infectious diseases, cancer, allergy and autoimmunity. Moreover, DNA shuffling and screening technologies can facilitate process development of vaccine manufacturing through increased expression of recombinant polypeptides and viruses. Therefore, DNA shuffling and screening technologies can overcome some of the challenges that vaccine development currently faces.

Slow Proton Transfer Coupled to Unfolding Explains the Puzzling Results of Single-Molecule Experiments on BBL, a Paradigmatic Downhill Folding Protein

PubMed Central

Cerminara, Michele; Campos, Luis A.; Ramanathan, Ravishankar; Muñoz, Victor

2013-01-01

A battery of thermodynamic, kinetic, and structural approaches has indicated that the small α-helical protein BBL folds-unfolds via the one-state downhill scenario. Yet, single-molecule fluorescence spectroscopy offers a more conflicting view. Single-molecule experiments at pH 6 show a unique half-unfolded conformational ensemble at mid denaturation, whereas other experiments performed at higher pH show a bimodal distribution, as expected for two-state folding. Here we use thermodynamic and laser T-jump kinetic experiments combined with theoretical modeling to investigate the pH dependence of BBL stability, folding kinetics and mechanism within the pH 6–11 range. We find that BBL unfolding is tightly coupled to the protonation of one of its residues with an apparent pKa of ∼7. Therefore, in chemical denaturation experiments around neutral pH BBL unfolds gradually, and also converts in binary fashion to the protonated species. Moreover, under the single-molecule experimental conditions (denaturant midpoint and 279 K), we observe that proton transfer is much slower than the ∼15 microseconds folding-unfolding kinetics of BBL. The relaxation kinetics is distinctly biphasic, and the overall relaxation time (i.e. 0.2–0.5 ms) becomes controlled by the proton transfer step. We then show that a simple theoretical model of protein folding coupled to proton transfer explains quantitatively all these results as well as the two sets of single-molecule experiments, including their more puzzling features. Interestingly, this analysis suggests that BBL unfolds following a one-state downhill folding mechanism at all conditions. Accordingly, the source of the bimodal distributions observed during denaturation at pH 7–8 is the splitting of the unique conformational ensemble of BBL onto two slowly inter-converting protonation species. Both, the unprotonated and protonated species unfold gradually (one-state downhill), but they exhibit different degree of unfolding at any given condition because the native structure is less stable for the protonated form. PMID:24205082

Optimization of thermochemolysis analysis conditions for the in situ detection of organic compounds in Martian soil with the Mars Organic Molecule Analyzer (MOMA) experiment

NASA Astrophysics Data System (ADS)

Morisson, Marietta; Buch, Arnaud; Szopa, Cyril; Raulin, François; Stambouli, Moncef

2017-04-01

Martian surface is exposed to harsh radiative and oxidative conditions which are destructive for organic molecules. That is why the future ExoMars rover will examine the molecular composition of samples acquired from depths down to two meters below the Martian surface, where organics may have been protected from radiative and oxidative degradation. The samples will then be analyzed by the Pyrolysis-Gas Chromatography-Mass Spectrometry (Pyr-GC-MS) operational mode of the Mars Organic Molecule Analyzer (MOMA) instrument. To prevent thermal alteration of organic molecules during pyrolysis, thermochemolysis with tetramethylammonium hydroxide (TMAH) will extract the organics from the mineral matrix and methylate the polar functional groups, allowing the volatilization of molecules at lower temperatures and protecting the most labile chemical groups from thermal degradation. This study has been carried out on a Martian regolith analogue (JSC-Mars-1) with a high organic content with the aim of optimizing the thermochemolysis temperature within operating conditions similar to the MOMA experiment ones. We also performed Pyrolysis-GC-MS analysis as a comparison. The results show that, unlike pyrolysis alone - which mainly produces aromatics, namely thermally altered molecules - thermochemolysis allows the extraction and identification of numerous organic molecules of astrobiological interest. They also show that the main compounds start to be detectable at low thermochemolysis temperatures ranging from 400°C to 600°C. However, we noticed that the more the temperature increases, the more the chromatograms are saturated with thermally evolved molecules leading to many coelutions and making identification difficult.

An integrated structure- and system-based framework to identify new targets of metabolites and known drugs

PubMed Central

Naveed, Hammad; Hameed, Umar S.; Harrus, Deborah; Bourguet, William; Arold, Stefan T.; Gao, Xin

2015-01-01

Motivation: The inherent promiscuity of small molecules towards protein targets impedes our understanding of healthy versus diseased metabolism. This promiscuity also poses a challenge for the pharmaceutical industry as identifying all protein targets is important to assess (side) effects and repositioning opportunities for a drug. Results: Here, we present a novel integrated structure- and system-based approach of drug-target prediction (iDTP) to enable the large-scale discovery of new targets for small molecules, such as pharmaceutical drugs, co-factors and metabolites (collectively called ‘drugs’). For a given drug, our method uses sequence order–independent structure alignment, hierarchical clustering and probabilistic sequence similarity to construct a probabilistic pocket ensemble (PPE) that captures promiscuous structural features of different binding sites on known targets. A drug’s PPE is combined with an approximation of its delivery profile to reduce false positives. In our cross-validation study, we use iDTP to predict the known targets of 11 drugs, with 63% sensitivity and 81% specificity. We then predicted novel targets for these drugs—two that are of high pharmacological interest, the peroxisome proliferator-activated receptor gamma and the oncogene B-cell lymphoma 2, were successfully validated through in vitro binding experiments. Our method is broadly applicable for the prediction of protein-small molecule interactions with several novel applications to biological research and drug development. Availability and implementation: The program, datasets and results are freely available to academic users at http://sfb.kaust.edu.sa/Pages/Software.aspx. Contact: xin.gao@kaust.edu.sa and stefan.arold@kaust.edu.sa Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26286808

Design of a Sensitive and Selective Electrochemical Aptasensor for the Determination of the Complementary cDNA of miRNA-145 Based on the Intercalation and Electrochemical Reduction of Doxorubicin.

PubMed

Mohamadi, Maryam; Mostafavi, Ali; Torkzadeh-Mahani, Masoud

2017-11-01

The aim of this research was the determination of a microRNA (miRNA) using a DNA electrochemical aptasensor. In this biosensor, the complementary complementary DNA (cDNA) of miRNA-145 (a sense RNA transcript) was the target strand and the cDNA of miRNA-145 was the probe strand. Both cDNAs can be the product of the reverse transcriptase-polymerase chain reaction of miRNA. The proposed aptasensor's function was based on the hybridization of target strands with probes immobilized on the surface of a working electrode and the subsequent intercalation of doxorubicin (DOX) molecules functioning as the electroactive indicators of any double strands that formed. Electrochemical transduction was performed by measuring the cathodic current resulting from the electrochemical reduction of the intercalated molecules at the electrode surface. In the experiment, because many DOX molecules accumulated on each target strand on the electrode surface, amplification was inherently easy, without a need for enzymatic or complicated amplification strategies. The proposed aptasensor also had the excellent ability to regenerate as a result of the melting of the DNA duplex. Moreover, the use of DNA probe strands obviated the challenges of working with an RNA probe, such as sensitivity to RNase enzyme. In addition to the linear relationship between the electrochemical signal and the concentration of the target strands that ranged from 2.0 to 80.0 nM with an LOD of 0.27 nM, the proposed biosensor was clearly capable of distinguishing between complementary (target strand) and noncomplementary sequences. The presented biosensor was successfully applied for the quantification of DNA strands corresponding to miRNA-145 in human serum samples.

Chinese hamster ovary K1 host cell enables stable cell line development for antibody molecules which are difficult to express in DUXB11-derived dihydrofolate reductase deficient host cell.

PubMed

Hu, Zhilan; Guo, Donglin; Yip, Shirley S M; Zhan, Dejin; Misaghi, Shahram; Joly, John C; Snedecor, Bradley R; Shen, Amy Y

2013-01-01

Therapeutic monoclonal antibodies (mAb) are often produced in Chinese hamster ovary (CHO) cells. Three commonly used CHO host cells for generating stable cell lines to produce therapeutic proteins are dihydrofolate reductase (DHFR) positive CHOK1, DHFR-deficient DG44, and DUXB11-based DHFR deficient CHO. Current Genentech commercial full-length antibody products have all been produced in the DUXB11-derived DHFR-deficient CHO host. However, it has been challenging to develop stable cell lines producing an appreciable amount of antibody proteins in the DUXB11-derived DHFR-deficient CHO host for some antibody molecules and the CHOK1 host has been explored as an alternative approach. In this work, stable cell lines were developed for three antibody molecules in both DUXB11-based and CHOK1 hosts. Results have shown that the best CHOK1 clones produce about 1 g/l for an antibody mAb1 and about 4 g/l for an antibody mAb2 in 14-day fed batch cultures in shake flasks. In contrast, the DUXB11-based host produced ∼0.1 g/l for both antibodies in the same 14-day fed batch shake flask production experiments. For an antibody mAb3, both CHOK1 and DUXB11 host cells can generate stable cell lines with the best clone in each host producing ∼2.5 g/l. Additionally, studies have shown that the CHOK1 host cell has a larger endoplasmic reticulum and higher mitochondrial mass. © 2013 American Institute of Chemical Engineers.

Optimal Superpositioning of Flexible Molecule Ensembles

PubMed Central

Gapsys, Vytautas; de Groot, Bert L.

2013-01-01

Analysis of the internal dynamics of a biological molecule requires the successful removal of overall translation and rotation. Particularly for flexible or intrinsically disordered peptides, this is a challenging task due to the absence of a well-defined reference structure that could be used for superpositioning. In this work, we started the analysis with a widely known formulation of an objective for the problem of superimposing a set of multiple molecules as variance minimization over an ensemble. A negative effect of this superpositioning method is the introduction of ambiguous rotations, where different rotation matrices may be applied to structurally similar molecules. We developed two algorithms to resolve the suboptimal rotations. The first approach minimizes the variance together with the distance of a structure to a preceding molecule in the ensemble. The second algorithm seeks for minimal variance together with the distance to the nearest neighbors of each structure. The newly developed methods were applied to molecular-dynamics trajectories and normal-mode ensembles of the Aβ peptide, RS peptide, and lysozyme. These new (to our knowledge) superpositioning methods combine the benefits of variance and distance between nearest-neighbor(s) minimization, providing a solution for the analysis of intrinsic motions of flexible molecules and resolving ambiguous rotations. PMID:23332072

Self-Assembled Core-Satellite Gold Nanoparticle Networks for Ultrasensitive Detection of Chiral Molecules by Recognition Tunneling Current.

PubMed

Zhang, Yuanchao; Liu, Jingquan; Li, Da; Dai, Xing; Yan, Fuhua; Conlan, Xavier A; Zhou, Ruhong; Barrow, Colin J; He, Jin; Wang, Xin; Yang, Wenrong

2016-05-24

Chirality sensing is a very challenging task. Here, we report a method for ultrasensitive detection of chiral molecule l/d-carnitine based on changes in the recognition tunneling current across self-assembled core-satellite gold nanoparticle (GNP) networks. The recognition tunneling technique has been demonstrated to work at the single molecule level where the binding between the reader molecules and the analytes in a nanojunction. This process was observed to generate a unique and sensitive change in tunneling current, which can be used to identify the analytes of interest. The molecular recognition mechanism between amino acid l-cysteine and l/d-carnitine has been studied with the aid of SERS. The different binding strength between homo- or heterochiral pairs can be effectively probed by the copper ion replacement fracture. The device resistance was measured before and after the sequential exposures to l/d-carnitine and copper ions. The normalized resistance change was found to be extremely sensitive to the chirality of carnitine molecule. The results suggested that a GNP networks device optimized for recognition tunneling was successfully built and that such a device can be used for ultrasensitive detection of chiral molecules.

Method for preparation and readout of polyatomic molecules in single quantum states

NASA Astrophysics Data System (ADS)

Patterson, David

2018-03-01

Polyatomic molecular ions contain many desirable attributes of a useful quantum system, including rich internal degrees of freedom and highly controllable coupling to the environment. To date, the vast majority of state-specific experimental work on molecular ions has concentrated on diatomic species. The ability to prepare and read out polyatomic molecules in single quantum states would enable diverse experimental avenues not available with diatomics, including new applications in precision measurement, sensitive chemical and chiral analysis at the single-molecule level, and precise studies of Hz-level molecular tunneling dynamics. While cooling the motional state of a polyatomic ion via sympathetic cooling with a laser-cooled atomic ion is straightforward, coupling this motional state to the internal state of the molecule has proven challenging. Here we propose a method for readout and projective measurement of the internal state of a trapped polyatomic ion. The method exploits the rich manifold of technically accessible rotational states in the molecule to realize robust state preparation and readout with far less stringent engineering than quantum logic methods recently demonstrated on diatomic molecules. The method can be applied to any reasonably small (≲10 atoms) polyatomic ion with an anisotropic polarizability.

Interplay between translational diffusion and large-amplitude angular jumps of water molecules

NASA Astrophysics Data System (ADS)

Liu, Chao; Zhang, Yangyang; Zhang, Jian; Wang, Jun; Li, Wenfei; Wang, Wei

2018-05-01

Understanding the microscopic mechanism of water molecular translational diffusion is a challenging topic in both physics and chemistry. Here, we report an investigation on the interplay between the translational diffusion and the large-amplitude angular jumps of water molecules in bulk water using molecular dynamics simulations. We found that large-amplitude angular jumps are tightly coupled to the translational diffusions. Particularly, we revealed that concurrent rotational jumps of spatially neighboring water molecules induce inter-basin translational jumps, which contributes to the fast component of the water translational diffusion. Consequently, the translational diffusion shows positional heterogeneity; i.e., the neighbors of the water molecules with inter-basin translational jumps have larger probability to diffuse by inter-basin translational jumps. Our control simulations showed that a model water molecule with moderate hydrogen bond strength can diffuse much faster than a simple Lennard-Jones particle in bulk water due to the capability of disturbing the hydrogen bond network of the surrounding water molecules. Our results added to the understanding of the microscopic picture of the water translational diffusion and demonstrated the unique features of water diffusion arising from their hydrogen bond network structure compared with those of the simple liquids.

Stabilization of protein-protein interactions in drug discovery.

PubMed

Andrei, Sebastian A; Sijbesma, Eline; Hann, Michael; Davis, Jeremy; O'Mahony, Gavin; Perry, Matthew W D; Karawajczyk, Anna; Eickhoff, Jan; Brunsveld, Luc; Doveston, Richard G; Milroy, Lech-Gustav; Ottmann, Christian

2017-09-01

PPIs are involved in every disease and specific modulation of these PPIs with small molecules would significantly improve our prospects of developing therapeutic agents. Both industry and academia have engaged in the identification and use of PPI inhibitors. However in comparison, the opposite strategy of employing small-molecule stabilizers of PPIs is underrepresented in drug discovery. Areas covered: PPI stabilization has not been exploited in a systematic manner. Rather, this concept validated by a number of therapeutically used natural products like rapamycin and paclitaxel has been shown retrospectively to be the basis of the activity of synthetic molecules originating from drug discovery projects among them lenalidomide and tafamidis. Here, the authors cover the growing number of synthetic small-molecule PPI stabilizers to advocate for a stronger consideration of this as a drug discovery approach. Expert opinion: Both the natural products and the growing number of synthetic molecules show that PPI stabilization is a viable strategy for drug discovery. There is certainly a significant challenge to adapt compound libraries, screening techniques and downstream methodologies to identify, characterize and optimize PPI stabilizers, but the examples of molecules reviewed here in our opinion justify these efforts.

Manipulating the motion of large molecules: Information from the molecular frame

NASA Astrophysics Data System (ADS)

Küpper, Jochen

2011-05-01

Large molecules have complex potential-energy surfaces with many local minima. They exhibit multiple stereoisomers, even at the low temperatures (~1 K) in a molecular beam, with rich intra- and intermolecular dynamics. Over the last years, we have developed methods to manipulate the motion of large, complex molecules and to select their quantum states. We have exploited this state-selectivity, for example, to spatially separate individual structural isomers of complex molecules and to demonstrate unprecedented degrees of laser alignment and mixed-field orientation of these molecules. Such clean, well-defined samples strongly benefit, or simply allow, novel experiments on the dynamics of complex molecules, for instance, femtosecond pump-probe measurements, X-ray or electron diffraction of molecular ensembles (including diffraction-from-within experiments), or tomographic reconstructions of molecular orbitals. These samples could also be very advantageous for metrology applications, such as, for example, matter-wave interferometry or the search for electroweak interactions in chiral molecules. Moreover, they provide an extreme level of control for stereo-dynamically controlled reaction dynamics. We have recently exploited these state-selected and oriented samples to measure photoelectron angular distributions in the molecular frame (MFPADs) from non-resonant femtosecond-laser photoionization and using the X-ray Free-Electron-Laser LCLS. We have also investigated X-ray diffraction imaging and, using ion momentum imaging, the induced radiation damage of these samples using the LCLS. This work was carried out within a collaboration for which J. Küpper, H. Chapman, and D. Rolles are spokespersons. The collaboration consists of CFEL (DESY, MPG, University Hamburg), Fritz-Haber-Institute Berlin, MPI Nuclear Physics Heidelberg, MPG Semi-conductor Lab, Aarhus University, FOM AMOLF Amsterdam, Lund University, MPI Medical Research Heidelberg, TU Berlin, Max Born Institute Berlin, and SLAC Menlo Park, CA, USA. The experiments were carried out using CAMP (designed and built by the MPG-ASG at CFEL) at the LCLS (operated by Stanford University on behalf of the US DOE).

Zero-mode waveguide nanophotonic structures for single molecule characterization

NASA Astrophysics Data System (ADS)

Crouch, Garrison M.; Han, Donghoon; Bohn, Paul W.

2018-05-01

Single-molecule characterization has become a crucial research tool in the chemical and life sciences, but limitations, such as limited concentration range, inability to control molecular distributions in space, and intrinsic phenomena, such as photobleaching, present significant challenges. Recent developments in non-classical optics and nanophotonics offer promising routes to mitigating these restrictions, such that even low affinity (K D ~ mM) biomolecular interactions can be studied. Here we introduce and review specific nanophotonic devices used to support single molecule studies. Optical nanostructures, such as zero-mode waveguides (ZMWs), are usually fabricated in thin gold or aluminum films and serve to confine the observation volume of optical microspectroscopy to attoliter to zeptoliter volumes. These simple nanostructures allow individual molecules to be isolated for optical and electrochemical analysis, even when the molecules of interest are present at high concentration (µM–mM) in bulk solution. Arrays of ZMWs may be combined with optical probes such as single molecule fluorescence, single molecule fluorescence resonance energy transfer, and fluorescence correlation spectroscopy for distributed analysis of large numbers of single-molecule reactions or binding events in parallel. Furthermore, ZMWs may be used as multifunctional devices, for example by combining optical and electrochemical functions in a single discrete architecture to achieve electrochemical ZMWs. In this review, we will describe the optical properties, fabrication, and applications of ZMWs for single-molecule studies, as well as the integration of ZMWs into systems for chemical and biochemical analysis.

Decelerating and Trapping Large Polar Molecules.

PubMed

Patterson, David

2016-11-18

Manipulating the motion of large polyatomic molecules, such as benzonitrile (C 6 H 5 CN), presents significant difficulties compared to the manipulation of diatomic molecules. Although recent impressive results have demonstrated manipulation, trapping, and cooling of molecules as large as CH 3 F, no general technique for trapping such molecules has been demonstrated, and cold neutral molecules larger than 5 atoms have not been trapped (M. Zeppenfeld, B. G. U. Englert, R. Glöckner, A. Prehn, M. Mielenz, C. Sommer, L. D. van Buuren, M. Motsch, G. Rempe, Nature 2012, 491, 570-573). In particular, extending Stark deceleration and electrostatic trapping to such species remains challenging. Here, we propose to combine a novel "asymmetric doublet state" Stark decelerator with recently demonstrated slow, cold, buffer-gas-cooled beams of closed-shell volatile molecules to realize a general system for decelerating and trapping samples of a broad range of volatile neutral polar prolate asymmetric top molecules. The technique is applicable to most stable volatile molecules in the 100-500 AMU range, and would be capable of producing trapped samples in a single rotational state and at a motional temperature of hundreds of mK. Such samples would immediately allow for spectroscopy of unprecedented resolution, and extensions would allow for further cooling and direct observation of slow intramolecular processes such as vibrational relaxation and Hertz-level tunneling dynamics. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Main challenges in demulsifier research and application

NASA Astrophysics Data System (ADS)

Zhang, Fusheng; Liu, Guoliang; Ma, Junhan; Ouyang, Jian; Yi, Xiaoling; Su, Huimin

2017-01-01

Main challenges in demulsifier research, such as demulsification of ASP flooding produced liquid, demulsification of heavy oil produced liquid, low temperature demulsification and fast demulsification, are summarized. Some importance technology routes to solve the challenges are proposed according to demulsification mechanisms and emulsion characteristics. The proposed routes include increasing aromaticity, molecular weight and branch degree of demulsifiers, and introducing double-function groups to demulsifiers for W/O and O/W emulsions, or groups with alkyl matching with alkyl carbon number of the crude oil into demulsifier molecule. The demulsification mechanisms of the above-mentioned research routes are described in detail.

Editorial overview: Omics

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

Barran, Perdita; Baker, Erin

The great complexity of biological systems and their environment poses similarly vast challenges for accurate analytical evaluations of their identity, structure and quantity. Post genomic science, has predicted much regarding the static populations of biological systems, but a further challenge for analysis is to test the accuracy of these predictions, as well as provide a better representation of the transient nature of the molecules of life. Accurate measurements of biological systems have wide applications for biological, forensic, biotechnological and healthcare fields. Therefore, the holy grail is to find a technique which can identify and quantify biological molecules with high throughput,more » sensitivity and robustness, as well evaluate molecular structure(s) in order to understand how the specific molecules interact and function. While wrapping all of these characteristics into one platform may sound difficult, ion mobility spectrometry (IMS) is addressing all of these challenges. Over the last decade, the number of analytical studies utilizing IMS for the evaluation of complex biological and environmental samples has greatly increased. In most cases IMS is coupled with mass spectrometry (IM-MS), but even alone IMS provides the unique capability of rapidly assessing a molecule’s structure, which can be extremely difficult with other techniques. The robustness of the IMS measurement is bourne out by its widespread use in security, environmental and military applications. The multidimensional IM-MS measurements however have been proven to be ever more powerful, as applied to complex mixtures as they enable the evaluation of both the structure and mass of every molecular component in a sample during a single measurement, without the need for continual reference calibration.« less

Mathematical inference and control of molecular networks from perturbation experiments

NASA Astrophysics Data System (ADS)

Mohammed-Rasheed, Mohammed

One of the main challenges facing biologists and mathematicians in the post genomic era is to understand the behavior of molecular networks and harness this understanding into an educated intervention of the cell. The cell maintains its function via an elaborate network of interconnecting positive and negative feedback loops of genes, RNA and proteins that send different signals to a large number of pathways and molecules. These structures are referred to as genetic regulatory networks (GRNs) or molecular networks. GRNs can be viewed as dynamical systems with inherent properties and mechanisms, such as steady-state equilibriums and stability, that determine the behavior of the cell. The biological relevance of the mathematical concepts are important as they may predict the differentiation of a stem cell, the maintenance of a normal cell, the development of cancer and its aberrant behavior, and the design of drugs and response to therapy. Uncovering the underlying GRN structure from gene/protein expression data, e.g., microarrays or perturbation experiments, is called inference or reverse engineering of the molecular network. Because of the high cost and time consuming nature of biological experiments, the number of available measurements or experiments is very small compared to the number of molecules (genes, RNA and proteins). In addition, the observations are noisy, where the noise is due to the measurements imperfections as well as the inherent stochasticity of genetic expression levels. Intra-cellular activities and extra-cellular environmental attributes are also another source of variability. Thus, the inference of GRNs is, in general, an under-determined problem with a highly noisy set of observations. The ultimate goal of GRN inference and analysis is to be able to intervene within the network, in order to force it away from undesirable cellular states and into desirable ones. However, it remains a major challenge to design optimal intervention strategies in order to affect the time evolution of molecular activity in a desirable manner. In this proposal, we address both the inference and control problems of GRNs. In the first part of the thesis, we consider the control problem. We assume that we are given a general topology network structure, whose dynamics follow a discrete-time Markov chain model. We subsequently develop a comprehensive framework for optimal perturbation control of the network. The aim of the perturbation is to drive the network away from undesirable steady-states and to force it to converge to a unique desirable steady-state. The proposed framework does not make any assumptions about the topology of the initial network (e.g., ergodicity, weak and strong connectivity), and is thus applicable to general topology networks. We define the optimal perturbation as the minimum-energy perturbation measured in terms of the Frobenius norm between the initial and perturbed networks. We subsequently demonstrate that there exists at most one optimal perturbation that forces the network into the desirable steady-state. In the event where the optimal perturbation does not exist, we construct a family of sub-optimal perturbations that approximate the optimal solution arbitrarily closely. In the second part of the thesis, we address the inference problem of GRNs from time series data. We model the dynamics of the molecules using a system of ordinary differential equations corrupted by additive white noise. For large-scale networks, we formulate the inference problem as a constrained maximum likelihood estimation problem. We derive the molecular interactions that maximize the likelihood function while constraining the network to be sparse. We further propose a procedure to recover weak interactions based on the Bayesian information criterion. For small-size networks, we investigated the inference of a globally stable 7-gene melanoma genetic regulatory network from genetic perturbation experiments. We considered five melanoma cell lines, who exhibit different motility/invasion behavior under the same perturbation experiment of gene Wnt5a. The results of the simulations validate both the steady state levels and the experimental data of the perturbation experiments of all five cell lines. The goal of this study is to answer important questions that link the response of the network to perturbations, as measured by the experiments, to its structure, i.e., connectivity. Answers to these questions shed novel insights on the structure of networks and how they react to perturbations.

Real-time visualization of soliton molecules with evolving behavior in an ultrafast fiber laser

NASA Astrophysics Data System (ADS)

Liu, Meng; Li, Heng; Luo, Ai-Ping; Cui, Hu; Xu, Wen-Cheng; Luo, Zhi-Chao

2018-03-01

Ultrafast fiber lasers have been demonstrated to be great platforms for the investigation of soliton dynamics. The soliton molecules, as one of the most fascinating nonlinear phenomena, have been a hot topic in the field of nonlinear optics in recent years. Herein, we experimentally observed the real-time evolving behavior of soliton molecule in an ultrafast fiber laser by using the dispersive Fourier transformation technology. Several types of evolving soliton molecules were obtained in our experiments, such as soliton molecules with monotonically or chaotically evolving phase, flipping and hopping phase. These results would be helpful to the communities interested in soliton nonlinear dynamics as well as ultrafast laser technologies.

Ab initio calculation of hyperfine splitting constants of molecules

NASA Astrophysics Data System (ADS)

Ohta, K.; Nakatsuji, H.; Hirao, K.; Yonezawa, T.

1980-08-01

Hyperfine splitting (hfs) constants of molecules, methyl, ethyl, vinyl, allyl, cyclopropyl, formyl, O3-, NH2, NO2, and NF2 radicals have been calculated by the pseudo-orbital (PO) theory, the unrestricted HF (UHF), projected UHF (PUHF) and single excitation (SE) CI theories. The pseudo-orbital (PO) theory is based on the symmetry-adapted-cluster (SAC) expansion proposed previously. Several contractions of the Gaussian basis sets of double-zeta accuracy have been examined. The UHF results were consistently too large to compare with experiments and the PUHF results were too small. For molecules studied here, the PO theory and SECI theory gave relatively close results. They were in fair agreement with experiments. The first-order spin-polarization self-consistency effect, which was shown to be important for atoms, is relatively small for the molecules. The present result also shows an importance of eliminating orbital-transformation dependence from conventional first-order perturbation calculations. The present calculations have explained well several important variations in the experimental hfs constants.

Entangled photons from single atoms and molecules

NASA Astrophysics Data System (ADS)

Nordén, Bengt

2018-05-01

The first two-photon entanglement experiment performed 50 years ago by Kocher and Commins (KC) provided isolated pairs of entangled photons from an atomic three-state fluorescence cascade. In view of questioning of Bell's theorem, data from these experiments are re-analyzed and shown sufficiently precise to confirm quantum mechanical and dismiss semi-classical theory without need for Bell's inequalities. Polarization photon correlation anisotropy (A) is useful: A is near unity as predicted quantum mechanically and well above the semi-classic range, 0 ⩽ A ⩽ 1 / 2 . Although yet to be found, one may envisage a three-state molecule emitting entangled photon pairs, in analogy with the KC atomic system. Antibunching in fluorescence from single molecules in matrix and entangled photons from quantum dots promise it be possible. Molecules can have advantages to parametric down-conversion as the latter photon distribution is Poissonian and unsuitable for producing isolated pairs of entangled photons. Analytical molecular applications of entangled light are also envisaged.

Ion-Molecule Reaction Dynamics

NASA Astrophysics Data System (ADS)

Meyer, Jennifer; Wester, Roland

2017-05-01

We review the recent advances in the investigation of the dynamics of ion-molecule reactions. During the past decade, the combination of single-collision experiments in crossed ion and neutral beams with the velocity map ion imaging detection technique has enabled a wealth of studies on ion-molecule reactions. These methods, in combination with chemical dynamics simulations, have uncovered new and unexpected reaction mechanisms, such as the roundabout mechanism and the subtle influence of the leaving group in anion-molecule nucleophilic substitution reactions. For this important class of reactions, as well as for many fundamental cation-molecule reactions, the information obtained with crossed-beam imaging is discussed. The first steps toward understanding micro-solvation of ion-molecule reaction dynamics are presented. We conclude with the presentation of several interesting directions for future research.