Morphological diagnostics of star formation in molecular clouds

NASA Astrophysics Data System (ADS)

Beaumont, Christopher Norris

Molecular clouds are the birth sites of all star formation in the present-day universe. They represent the initial conditions of star formation, and are the primary medium by which stars transfer energy and momentum back to parsec scales. Yet, the physical evolution of molecular clouds remains poorly understood. This is not due to a lack of observational data, nor is it due to an inability to simulate the conditions inside molecular clouds. Instead, the physics and structure of the interstellar medium are sufficiently complex that interpreting molecular cloud data is very difficult. This dissertation mitigates this problem, by developing more sophisticated ways to interpret morphological information in molecular cloud observations and simulations. In particular, I have focused on leveraging machine learning techniques to identify physically meaningful substructures in the interstellar medium, as well as techniques to inter-compare molecular cloud simulations to observations. These contributions make it easier to understand the interplay between molecular clouds and star formation. Specific contributions include: new insight about the sheet-like geometry of molecular clouds based on observations of stellar bubbles; a new algorithm to disambiguate overlapping yet morphologically distinct cloud structures; a new perspective on the relationship between molecular cloud column density distributions and the sizes of cloud substructures; a quantitative analysis of how projection effects affect measurements of cloud properties; and an automatically generated, statistically-calibrated catalog of bubbles identified from their infrared morphologies.

PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

EPA Science Inventory

The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

Molecular Rotation Signals: Molecule Chemistry and Particle Physics

NASA Astrophysics Data System (ADS)

Grabow, Jens-Uwe

2015-06-01

Molecules - large or small - are attractive academic resources, with numerous questions on their chemical behaviour as well as problems in fundamental physics now (or still) waiting to be answered: Targeted by high-resolution spectroscopy, a rotating molecular top can turn into a laboratory for molecule chemistry or a laboratory for particle physics. Once successfully entrained (many species - depending on size and chemical composition - have insufficient vapour pressures or are of transient nature, such that specifically designed pulsed-jet sources are required for their transfer into the gas phase or in-situ generation) into the collision-free environment of a supersonic-jet expansion, each molecular top comes with its own set of challenges, theoretically and experimentally: Multiple internal interactions are causing complicated energy level schemes and the resulting spectra will be rather difficult to predict theoretically. Experimentally, these spectra are difficult to assess and assign. With today's broad-banded chirp microwave techniques, finding and identifying such spectral features have lost their major drawback of being very time consuming for many molecules. For other molecules, the unrivalled resolution and sensitivity of the narrow-banded impulse microwave techniques provide a window to tackle - at the highest precision available to date - fundamental questions in physics, even particle physics - potentially beyond the standard model. Molecular charge distribution, properties of the chemical bond, details on internal dynamics and intermolecular interaction, the (stereo-chemical) molecular structure (including the possibility of their spatial separation) as well as potential evidence for tiny yet significant interactions encode their signature in pure molecular rotation subjected to time-domain microwave spectroscopic techniques. Ongoing exciting technical developments promise rapid progress. We present recent examples from Hannover, new directions, and an outlook at the future of molecular rotation spectroscopy.

NASA GSFC Science Symposium on Atomic and Molecular Physics

NASA Technical Reports Server (NTRS)

Bhatia, Anand K. (Editor)

2007-01-01

This document is the proceedings of a conference on atomic and molecular physics in honor of the retirements of Dr. Aaron Temkin and Dr. Richard Drachman. The conference contained discussions on electron, positron, atomic, and positronium physics, as well as a discussion on muon catalyzed fusion. This proceedings document also contains photographs taken at the symposium, as well as speeches and a short biography made in tribute to the retirees.

Computing the Ediz eccentric connectivity index of discrete dynamic structures

NASA Astrophysics Data System (ADS)

Wu, Hualong; Kamran Siddiqui, Muhammad; Zhao, Bo; Gan, Jianhou; Gao, Wei

2017-06-01

From the earlier studies in physical and chemical sciences, it is found that the physico-chemical characteristics of chemical compounds are internally connected with their molecular structures. As a theoretical basis, it provides a new way of thinking by analyzing the molecular structure of the compounds to understand their physical and chemical properties. In our article, we study the physico-chemical properties of certain molecular structures via computing the Ediz eccentric connectivity index from mathematical standpoint. The results we yielded mainly apply to the techniques of distance and degree computation of mathematical derivation, and the conclusions have guiding significance in physical engineering.

PREFACE: 7th Asian International Seminar on Atomic and Molecular Physics

NASA Astrophysics Data System (ADS)

Deshmukh, Pranawa C.; Chakraborty, Purushottam; Williams, Jim F.

2007-09-01

These proceedings arose from the 7th Asian International Seminar on Atomic and Molecular Physics (AISAMP) which was held at the Indian Institute of Technology, Madras from 4-7 December 2006. The history of the AISAMP has been reviewed by Takayanagi http://www.physics.iitm.ac.in/~aisamp7/history.html. This international seminar/conference series grew out of the Japan-China meetings which were launched in 1985, the fourth of which was held in 1992 and carried a second title: The First Asian International Seminar on Atomic and Molecular Physics (AISAMP), thus providing a formal medium for scientists in this part of the world to report periodically and exchange their scientific thoughts. The founding nations of Japan and China were joined subsequently by Korea, Taiwan, India and Australia. The aims of the symposia included bringing together leading experts and students of atomic and molecular physics, the discussion of important problems, learning and sharing modern techniques and expanding the horizons of modern atomic and molecular physics. The fields of interest ranged from atomic and molecular structure and dynamics to photon, electron and positron scattering, to quantum information processing, the effects of symmetry and many body interactions, laser cooling, cold traps, electric and magnetic fields and to atomic and molecular physics with synchrotron radiation. Particular interest was evident in new techniques and the changes of the physical properties from atomic to condensed matter. Details of the 7th AISAMP, including the topics for the special sessions and the full programme, are available online at the conference website http://www.physics.iitm.ac.in/~aisamp7/. In total, 95 presentations were made at the 7th AISAMP, these included the Invited Talks and Contributed Poster Presentations, of which 52 appear in the present Proceedings after review by expert referees, refereed to the usual standard of the Institute of Physics journal: Journal of Physics B: Atomic, Molecular and Optical Physics. We received extensive support from the Journal of Physics: Conference Series staff; Graham Douglas, in particular, has been of tremendous help. The 7th AISAMP was very well attended and was sponsored primarily by the host Indian Institute of Technology, Madras (Chennai), the Board of Research in Nuclear Sciences, (Department of Atomic Energy, Government of India), the Department of Science and Technology, (Government of India), and the Asian Office of Aerospace Research and Development (AOARD) of the US Air Force. There was support from various quarters—each was invaluable and added to the success of the 7th AISAMP. We are very grateful to all the sponsors. It is superfluous to add that guidance and active participation from several colleagues within the host Institute was the primary source of strength for the actual organization of the conference and the multitude of arrangements for the organization came from the young graduate students at the IIT-Madras. We hope that this volume of Journal of Physics: Conference Series will be referenced widely and that it will strengthen ties between various countries in the region in and around Asia, and also of course to all scientists in this field the world over. Pranawa C Deshmukh, Purushottam Chakraborty and Jim F Williams Editors Conference photograph

Rational chemical design of the next generation of molecular imaging probes based on physics and biology: mixing modalities, colors and signals

PubMed Central

Longmire, Michelle R.; Ogawa, Mikako; Choyke, Peter L.

2012-01-01

In recent years, numerous in vivo molecular imaging probes have been developed. As a consequence, much has been published on the design and synthesis of molecular imaging probes focusing on each modality, each type of material, or each target disease. More recently, second generation molecular imaging probes with unique, multi-functional, or multiplexed characteristics have been designed. This critical review focuses on (i) molecular imaging using combinations of modalities and signals that employ the full range of the electromagnetic spectra, (ii) optimized chemical design of molecular imaging probes for in vivo kinetics based on biology and physiology across a range of physical sizes, (iii) practical examples of second generation molecular imaging probes designed to extract complementary data from targets using multiple modalities, color, and comprehensive signals (277 references). PMID:21607237

Bright Coherent Optical Waveforms from the Infrared to the Vacuum Ultraviolet for Manipulation and Detection of Molecules

DTIC Science & Technology

2012-12-13

Margaret Murnane. Invited talk, ITAMP Winter School on Atomic, Molecular and Optical Physics ( Biosphere 2, AZ, January 2012). McElvain Lecture...Molecular and Optical Physics ( Biosphere 2, AZ, January 2012). McElvain Lecture, University of Wisconsin Chemistry Department, February 2012. Seminar

Physics in the Twentieth Century

ERIC Educational Resources Information Center

Weisskopf, Victor F.

1970-01-01

Provides a review of the great discoveries, theoretical concepts and development of physics in the 20th century. The growth and significance of diverse fields such as quantum theory, relativity theory, atomic physics, molecular physics, the physics of the solid state, nuclear physics, astrophysics, plasma physics, and particle physics are…

Theoretical and experimental studies in ultraviolet solar physics

NASA Technical Reports Server (NTRS)

Parkinson, W. H.; Reeves, E. M.

1975-01-01

The processes and parameters in atomic and molecular physics that are relevant to solar physics are investigated. The areas covered include: (1) measurement of atomic and molecular parameters that contribute to discrete and continous sources of opacity and abundance determinations in the sun; (2) line broadening and scattering phenomena; and (3) development of an ion beam spectroscopic source which is used for the measurement of electron excitation cross sections of transition region and coronal ions.

Physical re-examination of parameters on a molecular collisions-based diffusion model for diffusivity prediction in polymers.

PubMed

Ohashi, Hidenori; Tamaki, Takanori; Yamaguchi, Takeo

2011-12-29

Molecular collisions, which are the microscopic origin of molecular diffusive motion, are affected by both the molecular surface area and the distance between molecules. Their product can be regarded as the free space around a penetrant molecule defined as the "shell-like free volume" and can be taken as a characteristic of molecular collisions. On the basis of this notion, a new diffusion theory has been developed. The model can predict molecular diffusivity in polymeric systems using only well-defined single-component parameters of molecular volume, molecular surface area, free volume, and pre-exponential factors. By consideration of the physical description of the model, the actual body moved and which neighbor molecules are collided with are the volume and the surface area of the penetrant molecular core. In the present study, a semiempirical quantum chemical calculation was used to calculate both of these parameters. The model and the newly developed parameters offer fairly good predictive ability. © 2011 American Chemical Society

The Role of Molecular Weight and Temperature on the Elastic and Viscoelastic Properties of a Glassy Thermoplastic Polyimide

NASA Technical Reports Server (NTRS)

Nicholson, Lee M.; Whitley, Karen S.; Gates, Thomas S.

2001-01-01

Mechanical testing of the elastic and viscoelastic response of an advanced thermoplastic polyimide (LaRC-SI) with known variations in molecular weight was performed over a range of temperatures below the glass transition temperature. The notched tensile strength was shown to be a strong function of both molecular weight and temperature, whereas stiffness was only a strong function of temperature. A critical molecular weight was observed to occur at a weight average molecular weight of M, approx. 22,000 g/mol below which, the notched tensile strength decreases rapidly. This critical molecular weight transition is temperature-independent. Low, molecular weight materials tended to fail in a brittle manner, whereas high molecular weight materials exhibited ductile failure. Furthermore, low molecular weight materials have increased creep compliance and creep compliance rate, and are more sensitive to temperature than the high molecular weight materials. At long timescales (less than 1100 hours) physical aging serves to significantly decrease the creep compliance and creep rate of all the materials tested. Low molecular weight materials are less influenced by the effects of physical aging.

Physics: A Career for You?

ERIC Educational Resources Information Center

American Inst. of Physics, New York, NY.

Information is provided for students who may be interested in pursuing a career in physics. This information includes the type of work done and areas studied by physicists in the following areas: nuclear physics, solid-state physics, elementary-particle physics, atomic/molecular/electron physics, fluid/plasma physics, space/planetary physics,…

Physics Division annual review, 1 April 1975--31 March 1976. [ANL

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

Garvey, G. T.

1976-01-01

An overview is given of Physics Division activities in the following areas: the heavy-ion booster; medium-energy physics; heavy-ion physics; low-energy charged-particle physics; accelerator operations; neutron physics; theoretical nuclear physics, and atomic and molecular physics. A bibliography of publications amounts to 27 pages. (RWR)

Circumstellar radio molecular lines

NASA Technical Reports Server (NTRS)

NGUYEN-QUANG-RIEU

1987-01-01

Radio molecular lines appear to be useful probes into the stellar environment. Silicon oxide masers provide information on the physical conditions in the immediate vicinity of the stellar photosphere. Valuable information on the physics operating in the envelope of IRC + 10216 was recently obtained by high sensitivity observations and detailed theoretical analyses. Infrared speckle interferometry in the molecular lines and in the continuum is helpful in the investigation of the inner region of the envelope. These techniques are discussed in terms of late-type star mass loss.

Introduction of Entropy via the Boltzmann Distribution in Undergraduate Physical Chemistry: A Molecular Approach

ERIC Educational Resources Information Center

Kozliak, Evguenii I.

2004-01-01

A molecular approach for introducing entropy in undergraduate physical chemistry course and incorporating the features of Davies' treatment that meets the needs of the students but ignores the complexities of statistics and upgrades the qualitative, intuitive approach of Lambert for general chemistry to a semiquantitative treatment using Boltzmann…

From Gene to Protein: A 3-Week Intensive Course in Molecular Biology for Physical Scientists

ERIC Educational Resources Information Center

Nadeau, Jay L.

2009-01-01

This article describes a 3-week intensive molecular biology methods course based upon fluorescent proteins, which is successfully taught at the McGill University to advanced undergraduates and graduates in physics, chemical engineering, biomedical engineering, and medicine. No previous knowledge of biological terminology or methods is expected, so…

Influence of Acute and Chronic Exercise on Glucose Uptake

PubMed Central

Röhling, Martin; Herder, Christian; Stemper, Theodor; Müssig, Karsten

2016-01-01

Insulin resistance plays a key role in the development of type 2 diabetes. It arises from a combination of genetic predisposition and environmental and lifestyle factors including lack of physical exercise and poor nutrition habits. The increased risk of type 2 diabetes is molecularly based on defects in insulin signaling, insulin secretion, and inflammation. The present review aims to give an overview on the molecular mechanisms underlying the uptake of glucose and related signaling pathways after acute and chronic exercise. Physical exercise, as crucial part in the prevention and treatment of diabetes, has marked acute and chronic effects on glucose disposal and related inflammatory signaling pathways. Exercise can stimulate molecular signaling pathways leading to glucose transport into the cell. Furthermore, physical exercise has the potential to modulate inflammatory processes by affecting specific inflammatory signaling pathways which can interfere with signaling pathways of the glucose uptake. The intensity of physical training appears to be the primary determinant of the degree of metabolic improvement modulating the molecular signaling pathways in a dose-response pattern, whereas training modality seems to have a secondary role. PMID:27069930

International Journal of Molecular Science 2017 Best Paper Award.

PubMed

2017-11-02

The Editors of the International Journal of Molecular Sciences have established the Best Paper Award to recognize the most outstanding articles published in the areas of molecular biology, molecular physics and chemistry that have been published in the International Journal of Molecular Sciences. The prizes have been awarded annually since 2012 [...].

Call for papers for special issue of Journal of Molecular Spectroscopy focusing on "Frequency-comb spectroscopy"

NASA Astrophysics Data System (ADS)

Foltynowicz, Aleksandra; Picqué, Nathalie; Ye, Jun

2018-05-01

Frequency combs are becoming enabling tools for many applications in science and technology, beyond the original purpose of frequency metrology of simple atoms. The precisely evenly spaced narrow lines of a laser frequency comb inspire intriguing approaches to molecular spectroscopy, designed and implemented by a growing community of scientists. Frequency-comb spectroscopy advances the frontiers of molecular physics across the entire electro-magnetic spectrum. Used as frequency rulers, frequency combs enable absolute frequency measurements and precise line shape studies of molecular transitions, for e.g. tests of fundamental physics and improved determination of fundamental constants. As light sources interrogating the molecular samples, they dramatically improve the resolution, precision, sensitivity and acquisition time of broad spectral-bandwidth spectroscopy and open up new opportunities and applications at the leading edge of molecular spectroscopy and sensing.

Clustering the Orion B giant molecular cloud based on its molecular emission.

PubMed

Bron, Emeric; Daudon, Chloé; Pety, Jérôme; Levrier, François; Gerin, Maryvonne; Gratier, Pierre; Orkisz, Jan H; Guzman, Viviana; Bardeau, Sébastien; Goicoechea, Javier R; Liszt, Harvey; Öberg, Karin; Peretto, Nicolas; Sievers, Albrecht; Tremblin, Pascal

2018-02-01

Previous attempts at segmenting molecular line maps of molecular clouds have focused on using position-position-velocity data cubes of a single molecular line to separate the spatial components of the cloud. In contrast, wide field spectral imaging over a large spectral bandwidth in the (sub)mm domain now allows one to combine multiple molecular tracers to understand the different physical and chemical phases that constitute giant molecular clouds (GMCs). We aim at using multiple tracers (sensitive to different physical processes and conditions) to segment a molecular cloud into physically/chemically similar regions (rather than spatially connected components), thus disentangling the different physical/chemical phases present in the cloud. We use a machine learning clustering method, namely the Meanshift algorithm, to cluster pixels with similar molecular emission, ignoring spatial information. Clusters are defined around each maximum of the multidimensional Probability Density Function (PDF) of the line integrated intensities. Simple radiative transfer models were used to interpret the astrophysical information uncovered by the clustering analysis. A clustering analysis based only on the J = 1 - 0 lines of three isotopologues of CO proves suffcient to reveal distinct density/column density regimes ( n H ~ 100 cm -3 , ~ 500 cm -3 , and > 1000 cm -3 ), closely related to the usual definitions of diffuse, translucent and high-column-density regions. Adding two UV-sensitive tracers, the J = 1 - 0 line of HCO + and the N = 1 - 0 line of CN, allows us to distinguish two clearly distinct chemical regimes, characteristic of UV-illuminated and UV-shielded gas. The UV-illuminated regime shows overbright HCO + and CN emission, which we relate to a photochemical enrichment effect. We also find a tail of high CN/HCO + intensity ratio in UV-illuminated regions. Finer distinctions in density classes ( n H ~ 7 × 10 3 cm -3 ~ 4 × 10 4 cm -3 ) for the densest regions are also identified, likely related to the higher critical density of the CN and HCO + (1 - 0) lines. These distinctions are only possible because the high-density regions are spatially resolved. Molecules are versatile tracers of GMCs because their line intensities bear the signature of the physics and chemistry at play in the gas. The association of simultaneous multi-line, wide-field mapping and powerful machine learning methods such as the Meanshift clustering algorithm reveals how to decode the complex information available in these molecular tracers.

A Molecular-Level View of the Physical Stability of Amorphous Solid Dispersions

NASA Astrophysics Data System (ADS)

Yuan, Xiaoda

Many pharmaceutical compounds being developed in recent years are poorly soluble in water. This has led to insufficient oral bioavailability of many compounds in vitro. The amorphous formulation is one of the promising techniques to increase the oral bioavailability of these poorly water-soluble compounds. However, an amorphous drug substance is inherently unstable because it is a high energy form. In order to increase the physical stability, the amorphous drug is often formulated with a suitable polymer to form an amorphous solid dispersion. Previous research has suggested that the formation of an intimately mixed drug-polymer mixture contributes to the stabilization of the amorphous drug compound. The goal of this research is to better understand the role of miscibility, molecular interactions and mobility on the physical stability of amorphous solid dispersions. Methods were developed to detect different degrees of miscibility on nanometer scale and to quantify the extent of hydrogen-bonding interactions between the drug and the polymer. Miscibility, hydrogen-bonding interactions and molecular mobility were correlated with physical stability during a six-month period using three model systems. Overall, this research provides molecular-level insights into many factors that govern the physical stability of amorphous solid dispersions which can lead to a more effective design of stable amorphous formulations.

CLINICAL APPROACH TO THE DIAGNOSTIC EVALUATION OF HERDITARY AND ACQUIRED NEUROMUSCULAR DISEASES

PubMed Central

McDonald, Craig M.

2012-01-01

SYNOPSIS In the context of a neuromuscular disease diagnostic evaluation, the clinician still must be able to obtain a relevant patient and family history and perform focused general, musculoskeletal, neurologic and functional physical examinations to direct further diagnostic evaluations. Laboratory studies for hereditary neuromuscular diseases include relevant molecular genetic studies. The EMG and nerve conduction studies remain an extension of the physical examination and help to guide further diagnostic studies such as molecular genetic studies, and muscle and nerve biopsies. All diagnostic information needs to be interpreted not in isolation, but within the context of relevant historical information, family history, physical examination findings, and laboratory data, electrophysiologic findings, pathologic findings, and molecular genetic findings if obtained. PMID:22938875

Polymer Molecular Weight Analysis by [Superscript 1]H NMR Spectroscopy

ERIC Educational Resources Information Center

Izunobi, Josephat U.; Higginbotham, Clement L.

2011-01-01

The measurement and analysis of molecular weight and molecular weight distribution remain matters of fundamental importance for the characterization and physical properties of polymers. Gel permeation chromatography (GPC) is the most routinely used method for the molecular weight determination of polymers whereas matrix-assisted laser…

Molecular Weight and Molecular Weight Distributions in Synthetic Polymers.

ERIC Educational Resources Information Center

Ward, Thomas Carl

1981-01-01

Focuses on molecular weight and molecular weight distributions (MWD) and models for predicting MWD in a pedagogical way. In addition, instrumental methods used to characterize MWD are reviewed with emphasis on physical chemistry of each, including end-group determination, osmometry, light scattering, solution viscosity, fractionation, and…

New concepts for molecular magnets

NASA Astrophysics Data System (ADS)

Pilawa, Bernd

1999-03-01

Miller and Epstein (1994) define molecular magnets as magnetic materials which are prepared by the low-temperature methods of the preparative chemistry. This definition includes molecular crystals of neutral radicals, radical salts and charge transfer complexes as well as metal complexes and polymers with unpaired spins (Dormann 1995). The challenge of molecular magnets consists in tailoring magnetic properties by specific modifications of the molecular units. The combination of magnetism with mechanical or electrical properties of molecular compounds promise materials of high technical interest (Gatteschi 1994a and 1994b, Möhwald 1996) and both the chemical synthesis of new molecular materials with magnetic properties as well as the physical investigation and explanation of these properties is important, in order to achieve any progress. This work deals with the physical characterization of the magnetic properties of molecular materials. It is organized as follows. In the first part molecular crystals of neutral radicals are studied. After briefly discussing the general magnetic properties of these materials and after an overview over the physical principles of exchange interaction between organic radicals I focus on the interplay between the crystallographic structure and the magnetic properties of various derivatives of the verdazyl and nitronyl nitroxide radicals. The magnetic properties of metal complexes are the subject of the second part. After an overview over the experimental and theoretical tools which are used for the investigation of the magnetic properties I shortly discuss the exchange coupling of transition metal ions and the magnetic properties of complexes of two and three metal ions. Special emphasis is given to spin cluster compounds. Spin cluster denote complexes of many magnetic ions. They are attractive as building blocks of molecular magnets as well as magnetic model compounds for the study of spin frustration, molecular super-paramagnetism and quasi one-dimensional magnets.

Anisotropic Rotational Diffusion Studied by Nuclear Spin Relaxation and Molecular Dynamics Simulation: An Undergraduate Physical Chemistry Laboratory

ERIC Educational Resources Information Center

Fuson, Michael M.

2017-01-01

Laboratories studying the anisotropic rotational diffusion of bromobenzene using nuclear spin relaxation and molecular dynamics simulations are described. For many undergraduates, visualizing molecular motion is challenging. Undergraduates rarely encounter laboratories that directly assess molecular motion, and so the concept remains an…

The Physics and Physical Chemistry of Molecular Machines.

PubMed

Astumian, R Dean; Mukherjee, Shayantani; Warshel, Arieh

2016-06-17

The concept of a "power stroke"-a free-energy releasing conformational change-appears in almost every textbook that deals with the molecular details of muscle, the flagellar rotor, and many other biomolecular machines. Here, it is shown by using the constraints of microscopic reversibility that the power stroke model is incorrect as an explanation of how chemical energy is used by a molecular machine to do mechanical work. Instead, chemically driven molecular machines operating under thermodynamic constraints imposed by the reactant and product concentrations in the bulk function as information ratchets in which the directionality and stopping torque or stopping force are controlled entirely by the gating of the chemical reaction that provides the fuel for the machine. The gating of the chemical free energy occurs through chemical state dependent conformational changes of the molecular machine that, in turn, are capable of generating directional mechanical motions. In strong contrast to this general conclusion for molecular machines driven by catalysis of a chemical reaction, a power stroke may be (and often is) an essential component for a molecular machine driven by external modulation of pH or redox potential or by light. This difference between optical and chemical driving properties arises from the fundamental symmetry difference between the physics of optical processes, governed by the Bose-Einstein relations, and the constraints of microscopic reversibility for thermally activated processes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Essential Concepts and Underlying Theories from Physics, Chemistry, and Mathematics for "Biochemistry and Molecular Biology" Majors

ERIC Educational Resources Information Center

Wright, Ann; Provost, Joseph; Roecklein-Canfield, Jennifer A.; Bell, Ellis

2013-01-01

Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members from around the country. The workshops have focused on developing lists of Core Principles or Foundational Concepts in Biochemistry and Molecular Biology, a list of foundational skills, and foundational concepts from Physics, Chemistry,…

Correlation of physical properties with molecular structure for some dicyclic hydrocarbons having high thermal-energy release per unit volume

NASA Technical Reports Server (NTRS)

Wise, P H; Serijan, K T; Goodman, I A

1951-01-01

As part of a program to study the correlation between molecular structure and physical properties of high-density hydrocarbons, the net heats of combustion, melting points, boiling points, densities, and kinematic viscosities of some hydrocarbons in the 2-n-alkylbiphenyl, 1,1-diphenylalkane, diphenylalkane, 1,1-dicyclohexylalkane, and dicyclohexylalkane series are presented.

Nanoscale Electronics from a Molecular Perspective

DTIC Science & Technology

2012-01-19

Cyclohexanethiolate Self-Assembled Monolayers with Local Barrier Height Imaging, Journal of Physical Chemistry C, (07 2011): 0. doi: 2012/01/05 20:34:27...accepted for publication in the Journal of Physical Chemistry-C regarding the adsorption, ordering, and local work function measurements for...cyclohexanethiol on Au(111): Unveiling Molecular Adsorption Geometry in Cyclohexanethiolate Self-Assembled Monolayers with Local Barrier Height Imaging

The Utilization of Sensori-motor Experiences for Introducing Young Pupils to Molecular Motion: A Report of a Pilot Study.

ERIC Educational Resources Information Center

Hadzigeorgiou, Yannis

2002-01-01

Does a sensori-motor experience help a physics student understand the movement of molecules in solids, liquids, and gases? Students aged 9-10 were given either traditional demonstrations of solids, liquids, and gases and the variation of molecular motion with temperature (iconic presentation), or they were involved in physical activities as they…

Perspective: Reaches of chemical physics in biology.

PubMed

Gruebele, Martin; Thirumalai, D

2013-09-28

Chemical physics as a discipline contributes many experimental tools, algorithms, and fundamental theoretical models that can be applied to biological problems. This is especially true now as the molecular level and the systems level descriptions begin to connect, and multi-scale approaches are being developed to solve cutting edge problems in biology. In some cases, the concepts and tools got their start in non-biological fields, and migrated over, such as the idea of glassy landscapes, fluorescence spectroscopy, or master equation approaches. In other cases, the tools were specifically developed with biological physics applications in mind, such as modeling of single molecule trajectories or super-resolution laser techniques. In this introduction to the special topic section on chemical physics of biological systems, we consider a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and finally systems-level approaches, based on the contributions to this special issue. Chemical physicists can look forward to an exciting future where computational tools, analytical models, and new instrumentation will push the boundaries of biological inquiry.

Perspective: Reaches of chemical physics in biology

PubMed Central

Gruebele, Martin; Thirumalai, D.

2013-01-01

Chemical physics as a discipline contributes many experimental tools, algorithms, and fundamental theoretical models that can be applied to biological problems. This is especially true now as the molecular level and the systems level descriptions begin to connect, and multi-scale approaches are being developed to solve cutting edge problems in biology. In some cases, the concepts and tools got their start in non-biological fields, and migrated over, such as the idea of glassy landscapes, fluorescence spectroscopy, or master equation approaches. In other cases, the tools were specifically developed with biological physics applications in mind, such as modeling of single molecule trajectories or super-resolution laser techniques. In this introduction to the special topic section on chemical physics of biological systems, we consider a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and finally systems-level approaches, based on the contributions to this special issue. Chemical physicists can look forward to an exciting future where computational tools, analytical models, and new instrumentation will push the boundaries of biological inquiry. PMID:24089712

Dealing with the Challenges of Teaching Molecular Biophysics to Biochemistry Majors through an Heuristics-Based Approach

ERIC Educational Resources Information Center

Castanho, Miguel A. R. B.

2002-01-01

The main distinction between the overlapping fields of molecular biophysics and biochemistry resides in their different approaches to the same problems. Molecular biophysics makes more use of physical techniques and focuses on quantitative data. This difference encounters two difficult pedagogical challenges when teaching molecular biophysics to…

Clustering the Orion B giant molecular cloud based on its molecular emission

PubMed Central

Bron, Emeric; Daudon, Chloé; Pety, Jérôme; Levrier, François; Gerin, Maryvonne; Gratier, Pierre; Orkisz, Jan H.; Guzman, Viviana; Bardeau, Sébastien; Goicoechea, Javier R.; Liszt, Harvey; Öberg, Karin; Peretto, Nicolas; Sievers, Albrecht; Tremblin, Pascal

2017-01-01

Context Previous attempts at segmenting molecular line maps of molecular clouds have focused on using position-position-velocity data cubes of a single molecular line to separate the spatial components of the cloud. In contrast, wide field spectral imaging over a large spectral bandwidth in the (sub)mm domain now allows one to combine multiple molecular tracers to understand the different physical and chemical phases that constitute giant molecular clouds (GMCs). Aims We aim at using multiple tracers (sensitive to different physical processes and conditions) to segment a molecular cloud into physically/chemically similar regions (rather than spatially connected components), thus disentangling the different physical/chemical phases present in the cloud. Methods We use a machine learning clustering method, namely the Meanshift algorithm, to cluster pixels with similar molecular emission, ignoring spatial information. Clusters are defined around each maximum of the multidimensional Probability Density Function (PDF) of the line integrated intensities. Simple radiative transfer models were used to interpret the astrophysical information uncovered by the clustering analysis. Results A clustering analysis based only on the J = 1 – 0 lines of three isotopologues of CO proves suffcient to reveal distinct density/column density regimes (nH ~ 100 cm−3, ~ 500 cm−3, and > 1000 cm−3), closely related to the usual definitions of diffuse, translucent and high-column-density regions. Adding two UV-sensitive tracers, the J = 1 − 0 line of HCO+ and the N = 1 − 0 line of CN, allows us to distinguish two clearly distinct chemical regimes, characteristic of UV-illuminated and UV-shielded gas. The UV-illuminated regime shows overbright HCO+ and CN emission, which we relate to a photochemical enrichment effect. We also find a tail of high CN/HCO+ intensity ratio in UV-illuminated regions. Finer distinctions in density classes (nH ~ 7 × 103 cm−3 ~ 4 × 104 cm−3) for the densest regions are also identified, likely related to the higher critical density of the CN and HCO+ (1 – 0) lines. These distinctions are only possible because the high-density regions are spatially resolved. Conclusions Molecules are versatile tracers of GMCs because their line intensities bear the signature of the physics and chemistry at play in the gas. The association of simultaneous multi-line, wide-field mapping and powerful machine learning methods such as the Meanshift clustering algorithm reveals how to decode the complex information available in these molecular tracers. PMID:29456256

Physics in perspective. Volume 2, part A: The core subfields of physics

NASA Technical Reports Server (NTRS)

1972-01-01

Panel reports to the Survey Committee are presented to provide detailed technical background and documentation for committee findings, and to indicate the vitality and strength of the subfields of physics. Included are the core subfields of acoustics, optics, condensed matter, plasmas and fluids, atomic molecular and electron physics, nuclear physics, and elementary particle physics.

Charge exchange molecular ion source

DOEpatents

Vella, Michael C.

2003-06-03

Ions, particularly molecular ions with multiple dopant nucleons per ion, are produced by charge exchange. An ion source contains a minimum of two regions separated by a physical barrier and utilizes charge exchange to enhance production of a desired ion species. The essential elements are a plasma chamber for production of ions of a first species, a physical separator, and a charge transfer chamber where ions of the first species from the plasma chamber undergo charge exchange or transfer with the reactant atom or molecules to produce ions of a second species. Molecular ions may be produced which are useful for ion implantation.

Bringing the physical sciences into your cell biology research

PubMed Central

Robinson, Douglas N.; Iglesias, Pablo A.

2012-01-01

Historically, much of biology was studied by physicists and mathematicians. With the advent of modern molecular biology, a wave of researchers became trained in a new scientific discipline filled with the language of genes, mutants, and the central dogma. These new molecular approaches have provided volumes of information on biomolecules and molecular pathways from the cellular to the organismal level. The challenge now is to determine how this seemingly endless list of components works together to promote the healthy function of complex living systems. This effort requires an interdisciplinary approach by investigators from both the biological and the physical sciences. PMID:23112230

Bringing the physical sciences into your cell biology research.

PubMed

Robinson, Douglas N; Iglesias, Pablo A

2012-11-01

Historically, much of biology was studied by physicists and mathematicians. With the advent of modern molecular biology, a wave of researchers became trained in a new scientific discipline filled with the language of genes, mutants, and the central dogma. These new molecular approaches have provided volumes of information on biomolecules and molecular pathways from the cellular to the organismal level. The challenge now is to determine how this seemingly endless list of components works together to promote the healthy function of complex living systems. This effort requires an interdisciplinary approach by investigators from both the biological and the physical sciences.

Understanding selective molecular recognition in integrated carbon nanotube-polymer sensors by simulating physical analyte binding on carbon nanotube-polymer scaffolds.

PubMed

Lin, Shangchao; Zhang, Jingqing; Strano, Michael S; Blankschtein, Daniel

2014-08-28

Macromolecular scaffolds made of polymer-wrapped single-walled carbon nanotubes (SWCNTs) have been explored recently (Zhang et al., Nature Nanotechnology, 2013) as a new class of molecular-recognition motifs. However, selective analyte recognition is still challenging and lacks the underlying fundamental understanding needed for its practical implementation in biological sensors. In this report, we combine coarse-grained molecular dynamics (CGMD) simulations, physical adsorption/binding theories, and photoluminescence (PL) experiments to provide molecular insight into the selectivity of such sensors towards a large set of biologically important analytes. We find that the physical binding affinities of the analytes on a bare SWCNT partially correlate with their distribution coefficients in a bulk water/octanol system, suggesting that the analyte hydrophobicity plays a key role in determining the binding affinities of the analytes considered, along with the various specific interactions between the analytes and the polymer anchor groups. Two distinct categories of analytes are identified to demonstrate a complex picture for the correlation between optical sensor signals and the simulated binding affinities. Specifically, a good correlation was found between the sensor signals and the physical binding affinities of the three hormones (estradiol, melatonin, and thyroxine), the neurotransmitter (dopamine), and the vitamin (riboflavin) to the SWCNT-polymer scaffold. The four amino acids (aspartate, glycine, histidine, and tryptophan) and the two monosaccharides (fructose and glucose) considered were identified as blank analytes which are unable to induce sensor signals. The results indicate great success of our physical adsorption-based model in explaining the ranking in sensor selectivities. The combined framework presented here can be used to screen and select polymers that can potentially be used for creating synthetic molecular recognition motifs.

Constraint methods that accelerate free-energy simulations of biomolecules.

PubMed

Perez, Alberto; MacCallum, Justin L; Coutsias, Evangelos A; Dill, Ken A

2015-12-28

Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann's law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.

Warm neutral halos around molecular clouds. VI - Physical and chemical modeling

NASA Technical Reports Server (NTRS)

Andersson, B.-G.; Wannier, P. G.

1993-01-01

A combined physical and chemical modeling of the halos around molecular clouds is presented, with special emphasis on the H-to-H2 transition. On the basis of H I 21 cm observations, it is shown that the halos are extended. A physical model is employed in conjunction with a chemistry code to provide a self-consistent description of the gas. The radiative transfer code provides a check with H I, CO, and OH observations. It is concluded that the warm neutral halos are not gravitationally bound to the underlying molecular clouds and are isobaric. It is inferred from the observed extent of the H I envelopes and the large observed abundance of OH in them that the generally accepted rate for H2 information on grains is too large by a factor of two to three.

Nanostructured silicon membranes for control of molecular transport.

PubMed

Srijanto, Bernadeta R; Retterer, Scott T; Fowlkes, Jason D; Doktycz, Mitchel J

2010-11-01

A membrane that allows selective transport of molecular species requires precise engineering on the nanoscale. Membrane permeability can be tuned by controlling the physical structure and surface chemistry of the pores. Here, a combination of electron beam and optical lithography, along with cryogenic deep reactive ion etching, has been used to fabricate silicon membranes that are physically robust, have uniform pore sizes, and are directly integrated into a microfluidic network. Additional reductions in pore size were achieved using plasma enhanced chemical vapor deposition and atomic layer deposition of silicon dioxide to coat membrane surfaces. Cross sectioning of the membranes using focused ion beam milling was used to determine the physical shape of the membrane pores before and after coating. Functional characterization of the membranes was performed by using quantitative fluorescence microscopy to document the transport of molecular species across the membrane.

When physics and biology meet: the nanoscale case.

PubMed

Bueno, Otávio

2011-06-01

As an illustration of the complexities involved in connecting physics and molecular biology at the nanoscale, in this paper I discuss two case studies from nanoscience. The first examines the use of a biological structure (DNA) to build nanostructures in a controlled way. The second discusses the attempt to build a single molecular wire, and then decide whether such a wire is indeed conducting. After presenting the central features of each case study, I examine the role played in them by microscopic imaging, the different styles of reasoning involved, and the various theoretical, methodological, and axiological differences. I conclude by arguing that, except for the probe microscopes that are used, there is very little in common between the two cases. At the nanoscale, physics and molecular biology seem to meet in a non-unified way. Copyright © 2010 Elsevier Ltd. All rights reserved.

Quantum and semiclassical spin networks: from atomic and molecular physics to quantum computing and gravity

NASA Astrophysics Data System (ADS)

Aquilanti, Vincenzo; Bitencourt, Ana Carla P.; Ferreira, Cristiane da S.; Marzuoli, Annalisa; Ragni, Mirco

2008-11-01

The mathematical apparatus of quantum-mechanical angular momentum (re)coupling, developed originally to describe spectroscopic phenomena in atomic, molecular, optical and nuclear physics, is embedded in modern algebraic settings which emphasize the underlying combinatorial aspects. SU(2) recoupling theory, involving Wigner's 3nj symbols, as well as the related problems of their calculations, general properties, asymptotic limits for large entries, nowadays plays a prominent role also in quantum gravity and quantum computing applications. We refer to the ingredients of this theory—and of its extension to other Lie and quantum groups—by using the collective term of 'spin networks'. Recent progress is recorded about the already established connections with the mathematical theory of discrete orthogonal polynomials (the so-called Askey scheme), providing powerful tools based on asymptotic expansions, which correspond on the physical side to various levels of semi-classical limits. These results are useful not only in theoretical molecular physics but also in motivating algorithms for the computationally demanding problems of molecular dynamics and chemical reaction theory, where large angular momenta are typically involved. As for quantum chemistry, applications of these techniques include selection and classification of complete orthogonal basis sets in atomic and molecular problems, either in configuration space (Sturmian orbitals) or in momentum space. In this paper, we list and discuss some aspects of these developments—such as for instance the hyperquantization algorithm—as well as a few applications to quantum gravity and topology, thus providing evidence of a unifying background structure.

Molecular Dynamics Simulations of Simple Liquids

ERIC Educational Resources Information Center

Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.

2004-01-01

An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.

Measurement of surface stay times for physical adsorption of gases. Ph.D. Thesis - Va. Univ.; [using molecular beam time of flight technique

NASA Technical Reports Server (NTRS)

Wilmoth, R. G.

1973-01-01

A molecular beam time-of-flight technique is studied as a means of determining surface stay times for physical adsorption. The experimental approach consists of pulsing a molecular beam, allowing the pulse to strike an adsorbing surface and detecting the molecular pulse after it has subsequently desorbed. The technique is also found to be useful for general studies of adsorption under nonequilibrium conditions including the study of adsorbate-adsorbate interactions. The shape of the detected pulse is analyzed in detail for a first-order desorption process. For mean stay times, tau, less than the mean molecular transit times involved, the peak of the detected pulse is delayed by an amount approximately equal to tau. For tau much greater than these transit times, the detected pulse should decay as exp(-t/tau). However, for stay times of the order of the transit times, both the molecular speed distributions and the incident pulse duration time must be taken into account.

Kinesin Motor Enzymology: Chemistry, Structure, and Physics of Nanoscale Molecular Machines.

PubMed

Cochran, J C

2015-09-01

Molecular motors are enzymes that convert chemical potential energy into controlled kinetic energy for mechanical work inside cells. Understanding the biophysics of these motors is essential for appreciating life as well as apprehending diseases that arise from motor malfunction. This review focuses on kinesin motor enzymology with special emphasis on the literature that reports the chemistry, structure and physics of several different kinesin superfamily members.

Modelling of Molecular Structures and Properties. Proceedings of the International Meeting of Physical Chemistry on Modeling of Molecular Structures and Properties in Physical Chemistry and Biophysics Organized by the Division de Chimie Physique of the Societe Francaise de Chimie Held in Nancy, France on 11-15 September 1989

DTIC Science & Technology

1990-01-01

expert systems, "intelligent" computer-aided instruction , symbolic learning . These aspects will be discussed, focusing on the specific problems the...VLSI chips) according to preliminary specifications. Finally ES are also used in computer-aided instruction (CAI) due to their ability of... instructions to process controllers), academic teaching (for mathematics , physics, foreign language, etc.). Domains of application The different

Influence of galactic arm scale dynamics on the molecular composition of the cold and dense ISM. I. Observed abundance gradients in dense clouds

NASA Astrophysics Data System (ADS)

Ruaud, M.; Wakelam, V.; Gratier, P.; Bonnell, I. A.

2018-04-01

Aim. We study the effect of large scale dynamics on the molecular composition of the dense interstellar medium during the transition between diffuse to dense clouds. Methods: We followed the formation of dense clouds (on sub-parsec scales) through the dynamics of the interstellar medium at galactic scales. We used results from smoothed particle hydrodynamics (SPH) simulations from which we extracted physical parameters that are used as inputs for our full gas-grain chemical model. In these simulations, the evolution of the interstellar matter is followed for 50 Myr. The warm low-density interstellar medium gas flows into spiral arms where orbit crowding produces the shock formation of dense clouds, which are held together temporarily by the external pressure. Results: We show that depending on the physical history of each SPH particle, the molecular composition of the modeled dense clouds presents a high dispersion in the computed abundances even if the local physical properties are similar. We find that carbon chains are the most affected species and show that these differences are directly connected to differences in (1) the electronic fraction, (2) the C/O ratio, and (3) the local physical conditions. We argue that differences in the dynamical evolution of the gas that formed dense clouds could account for the molecular diversity observed between and within these clouds. Conclusions: This study shows the importance of past physical conditions in establishing the chemical composition of the dense medium.

Prospects for Physics in the 1990's Surveyed.

ERIC Educational Resources Information Center

Robinson, Arthur L.

1986-01-01

A National Academy of Science report ("Physics Through the 1990's") says that American physics has been a highly diversified and productive enterprise, but continued excellence cannot be taken for granted. Progress in six subfields (elementary particle, nuclear, condensed-matter, atomic/molecular, plasma/fluid, and gravitation/cosmology physics)…

Mistakes and Molecular Evolution.

ERIC Educational Resources Information Center

Trevors, J. T.

1998-01-01

Examines the role mistakes play in the molecular evolution of bacteria. Discusses the interacting physical, chemical, and biological factors that cause changes in DNA and play a role in prokaryotic evolution. (DDR)

Physical conditions in molecular clouds

NASA Technical Reports Server (NTRS)

Evans, Neal J., II

1989-01-01

Recent developments have complicated the picture of the physical conditions in molecular clouds. The discoveries of widespread emission from high-J lines of CD and 12-micron IRAS emission have revealed the presence of considerably hotter gas and dust near the surfaces of molecular clouds. These components can complicate interpretation of the bulk of the cloud gas. Commonly assumed relations between column density or mean density and cloud size are called into question by conflicting results and by consideration of selection effects. Analysis of density and density structure through molecular excitation has shown that very high densities exist in star formation regions, but unresolved structure and possible chemical effects complicate the interpretation. High resolution far-IR and submillimeter observations offer a complementary approach and are beginning to test theoretical predictions of density gradients in clouds.

Study of Molecular Clouds, Variable Stars and Related Topics at NUU and UBAI

NASA Astrophysics Data System (ADS)

Hojaev, A. S.

2017-07-01

The search of young PMS stars made by our team at Maidanak, Lulin and Beijing observatories, especially in NGC 6820/23 area, as well as monitoring of a sample of open clusters will be described and results will be presented. We consider physical conditions in different star forming regions, particularly in TDC and around Vul OB1, estimate SFE and SFR, energy balance and instability processes in these regions. We also reviewed all data on molecular clouds in the Galaxy and in other galaxies where the clouds were observed to prepare general catalog of molecular clouds, to study physical conditions, unsteadiness and possible star formation in them, the formation and evolution of molecular cloud systems, to analyze their role in formation of different types of galaxies and structural features therein.

Evaluating experimental molecular physics studies of radiation damage in DNA*

NASA Astrophysics Data System (ADS)

Śmiałek, Małgorzata A.

2016-11-01

The field of Atomic and Molecular Physics (AMP) is a mature field exploring the spectroscopy, excitation, ionisation of atoms and molecules in all three phases. Understanding of the spectroscopy and collisional dynamics of AMP has been fundamental to the development and application of quantum mechanics and is applied across a broad range of disparate disciplines including atmospheric sciences, astrochemistry, combustion and environmental science, and in central to core technologies such as semiconductor fabrications, nanotechnology and plasma processing. In recent years the molecular physics also started significantly contributing to the area of the radiation damage at molecular level and thus cancer therapy improvement through both experimental and theoretical advances, developing new damage measurement and analysis techniques. It is therefore worth to summarise and highlight the most prominent findings from the AMP community that contribute towards better understanding of the fundamental processes in biologically-relevant systems as well as to comment on the experimental challenges that were met for more complex investigation targets. Contribution to the Topical Issue "Low-Energy Interactions related to Atmospheric and Extreme Conditions", edited by S. Ptasinska, M. Smialek-Telega, A. Milosavljevic, B. Sivaraman.

Imaging Multi-Particle Atomic and Molecular Dynamics

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

Landers, Allen

2016-02-12

Final Report for Grant Number: DE- FG02-10ER16146 This grant supported research in basic atomic, molecular and optical physics related to the interactions of atoms and molecules with photons and electrons. The duration of the grant was the 5 year period from 4/1/2010 – 10/31/2015. All of the support from the grant was used to pay salaries of the PI, graduate students, and undergraduates and travel to conferences and meetings. The results were in the form of publications in peer reviewed journals. There were 20 peer reviewed publications over these 5 years with 2 of the publications in Physical Review Lettersmore » and 1 in Nature; all of the other articles were in respected peer reviewed journals (Physical Review A, New Journal of Physics, Journal of Physics B ...).« less

Clustering the Orion B giant molecular cloud based on its molecular emission

NASA Astrophysics Data System (ADS)

Bron, Emeric; Daudon, Chloé; Pety, Jérôme; Levrier, François; Gerin, Maryvonne; Gratier, Pierre; Orkisz, Jan H.; Guzman, Viviana; Bardeau, Sébastien; Goicoechea, Javier R.; Liszt, Harvey; Öberg, Karin; Peretto, Nicolas; Sievers, Albrecht; Tremblin, Pascal

2018-02-01

Context. Previous attempts at segmenting molecular line maps of molecular clouds have focused on using position-position-velocity data cubes of a single molecular line to separate the spatial components of the cloud. In contrast, wide field spectral imaging over a large spectral bandwidth in the (sub)mm domain now allows one to combine multiple molecular tracers to understand the different physical and chemical phases that constitute giant molecular clouds (GMCs). Aims: We aim at using multiple tracers (sensitive to different physical processes and conditions) to segment a molecular cloud into physically/chemically similar regions (rather than spatially connected components), thus disentangling the different physical/chemical phases present in the cloud. Methods: We use a machine learning clustering method, namely the Meanshift algorithm, to cluster pixels with similar molecular emission, ignoring spatial information. Clusters are defined around each maximum of the multidimensional probability density function (PDF) of the line integrated intensities. Simple radiative transfer models were used to interpret the astrophysical information uncovered by the clustering analysis. Results: A clustering analysis based only on the J = 1-0 lines of three isotopologues of CO proves sufficient to reveal distinct density/column density regimes (nH 100 cm-3, 500 cm-3, and >1000 cm-3), closely related to the usual definitions of diffuse, translucent and high-column-density regions. Adding two UV-sensitive tracers, the J = 1-0 line of HCO+ and the N = 1-0 line of CN, allows us to distinguish two clearly distinct chemical regimes, characteristic of UV-illuminated and UV-shielded gas. The UV-illuminated regime shows overbright HCO+ and CN emission, which we relate to a photochemical enrichment effect. We also find a tail of high CN/HCO+ intensity ratio in UV-illuminated regions. Finer distinctions in density classes (nH 7 × 103 cm-3, 4 × 104 cm-3) for the densest regions are also identified, likely related to the higher critical density of the CN and HCO+ (1-0) lines. These distinctions are only possible because the high-density regions are spatially resolved. Conclusions: Molecules are versatile tracers of GMCs because their line intensities bear the signature of the physics and chemistry at play in the gas. The association of simultaneous multi-line, wide-field mapping and powerful machine learning methods such as the Meanshift clustering algorithm reveals how to decode the complex information available in these molecular tracers. Data products associated with this paper are available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/610/A12 and at http://www.iram.fr/ pety/ORION-B

Molecular Iodine Fluorescence Using a Green Helium-Neon Laser

ERIC Educational Resources Information Center

Williamson, J. Charles

2011-01-01

Excitation of molecular iodine vapor with a green (543.4 nm) helium-neon laser produces a fluorescence spectrum that is well suited for the upper-level undergraduate physical chemistry laboratory. Application of standard evaluation techniques to the spectrum yields ground electronic-state molecular parameters in good agreement with literature…

Integrating a Smartphone and Molecular Modeling for Determining the Binding Constant and Stoichiometry Ratio of the Iron(II)-Phenanthroline Complex: An Activity for Analytical and Physical Chemistry Laboratories

ERIC Educational Resources Information Center

de Morais, Camilo de L. M.; Silva, Se´rgio R. B.; Vieira, Davi S.; Lima, Ka´ssio M. G.

2016-01-01

The binding constant and stoichiometry ratio for the formation of iron(II)-(1,10-phenanthroline) or iron(II)-o-phenanthroline complexes has been determined by a combination of a low-cost analytical method using a smartphone and a molecular modeling method as a laboratory experiment designed for analytical and physical chemistry courses. Intensity…

Physical Properties of Low-Molecular Weight Polydimethylsiloxane Fluids

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

Roberts, Christine Cardinal; Graham, Alan; Nemer, Martin

Physical property measurements including viscosity, density, thermal conductivity, and heat capacity of low-molecular weight polydimethylsiloxane (PDMS) fluids were measured over a wide temperature range (-50°C to 150°C when possible). Properties of blends of 1 cSt and 20 cSt PDMS fluids were also investigated. Uncertainties in the measurements are cited. These measurements will provide greater fidelity predictions of environmental sensing device behavior in hot and cold environments.

Boundary conditions for the paleoenvironment: Chemical and Physical Processes in dense interstellar clouds

NASA Technical Reports Server (NTRS)

Irvine, W. M.; Schloerb, F. P.; Ziurys, L. M.

1986-01-01

The present research includes searches for important new interstellar constituents; observations relevant to differentiating between different models for the chemical processes that are important in the interstellar environment; and coordinated studies of the chemistry, physics, and dynamics of molecular clouds which are the sites or possible future sites of star formation. Recent research has included the detection and study of four new interstellar molecules; searches which have placed upper limits on the abundance of several other potential constituents of interstellar clouds; quantitative studies of comparative molecular abundances in different types of interstellar clouds; investigation of reaction pathways for astrochemistry from a comparison of theory and the observed abundance of related species such as isomers and isotopic variants; studies of possible tracers of energenic events related to star formation, including silicon and sulfur containing molecules; and mapping of physical, chemical, and dynamical properties over extended regions of nearby cold molecular clouds.

Molecular physics. Production of trilobite Rydberg molecule dimers with kilo-Debye permanent electric dipole moments.

PubMed

Booth, D; Rittenhouse, S T; Yang, J; Sadeghpour, H R; Shaffer, J P

2015-04-03

Permanent electric dipole moments are important for understanding symmetry breaking in molecular physics, control of chemical reactions, and realization of strongly correlated many-body quantum systems. However, large molecular permanent electric dipole moments are challenging to realize experimentally. We report the observation of ultralong-range Rydberg molecules with bond lengths of ~100 nanometers and kilo-Debye permanent electric dipole moments that form when an ultracold ground-state cesium (Cs) atom becomes bound within the electronic cloud of an extended Cs electronic orbit. The electronic character of this hybrid class of "trilobite" molecules is dominated by degenerate Rydberg manifolds, making them difficult to produce by conventional photoassociation. We used detailed coupled-channel calculations to reproduce their properties quantitatively. Our findings may lead to progress in ultracold chemistry and strongly correlated many-body physics. Copyright © 2015, American Association for the Advancement of Science.

Production of high molecular weight polylactic acid

DOEpatents

Bonsignore, Patrick V.

1995-01-01

A degradable high molecular weight poly(lactic acid). A poly(lactic acid) has a terminal end group of one of carboxyl or hydroxyl groups with low molecular weight poly(lactic acid) units coupled with linking agents of di-isocyanates, bis-epoxides, bis-oxazolines and bis-ortho esters. The resulting high molecular weight poly(lactic acid) can be used for applications taking advantage of the improved physical properties.

PSPP: A Protein Structure Prediction Pipeline for Computing Clusters

DTIC Science & Technology

2009-07-01

Evanseck JD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B 102...dimensional (3-D) protein structures are critical for the understanding of molecular mechanisms of living systems. Traditionally, X-ray crystallography...disordered proteins are often responsible for molecular recognition, molecular assembly, protein modifica- tion, and entropic chain activities in organisms [26

Time-resolved molecular imaging

NASA Astrophysics Data System (ADS)

Xu, Junliang; Blaga, Cosmin I.; Agostini, Pierre; DiMauro, Louis F.

2016-06-01

Time-resolved molecular imaging is a frontier of ultrafast optical science and physical chemistry. In this article, we review present and future key spectroscopic and microscopic techniques for ultrafast imaging of molecular dynamics and show their differences and connections. The advent of femtosecond lasers and free electron x-ray lasers bring us closer to this goal, which eventually will extend our knowledge about molecular dynamics to the attosecond time domain.

Understanding molecular structure from molecular mechanics.

PubMed

Allinger, Norman L

2011-04-01

Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

Molecular machines open cell membranes

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

Molecular machines open cell membranes.

PubMed

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

2017-08-30

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

Molecular/clinical correlations in females with fragile X

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

Sobesky, W.E.; Riddle, J.; Hagerman, R.J.

1996-08-09

Females who are affected by fragile X syndrome (FXS) can have significant physical, neuropsychological and emotional involvement. This study was designed to explore the relationships between these three domains and to learn how the degree of involvement in each of these phenotypic areas relates to molecular parameters including CGG repeat length and activation ratio (the proportion of normal FMR1 alleles on the active X chromosome). Three groups of females were studied: 35 women who grew up in a fragile X family but do not carry an FMR1 mutation, 92 women with a premutation, and 29 women with a full mutation.more » Correlations between neurocognitive, physical and emotional traits were calculated for each of the three groups. Within the full mutation group significant correlations were seen between schizotypal traits and full scale IQ. The Lie scale was significantly correlated with the physical findings index. The activation ratio correlated significantly with the measure of executive function (r = .50, P = .01). There was a trend toward correlations of activation ratio with the physical index score, outer ear prominence and IQ. CGG repeat number significantly correlated only with the physical index (r = .44, P = .0 1). Thus, activation ratio may be the more pertinent molecular parameter in full mutation women in determining the degree of cognitive and physical phenotypic involvement. 29 refs., 2 tabs.« less

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

Inokuti, M.; Rau, A. R. P.; Physics

With the passing of Ugo Fano on 13 February 2001, Comments on Atomic and Molecular Physics lost a longtime correspondent since its founding in 1969. A broader community dearly misses a great theoretical physicist. The present tribute is designed in a special way appropriate for this journal, in view of other documents describing Fano's life and work. It is accompanied by a curriculum vitae, which shows the span of a rich professional life. We shall concentrate on his accomplishments in atomic and molecular physics, leaving aside contributions to radiation physics and other areas. We also present a list of hismore » publications, which should be useful as a resource material.« less

Living matter—nexus of physics and biology in the 21st century

PubMed Central

Gardel, Margaret L.

2012-01-01

Cells are made up of complex assemblies of cytoskeletal proteins that facilitate force transmission from the molecular to cellular scale to regulate cell shape and force generation. The “living matter” formed by the cytoskeleton facilitates versatile and robust behaviors of cells, including their migration, adhesion, division, and morphology, that ultimately determine tissue architecture and mechanics. Elucidating the underlying physical principles of such living matter provides great opportunities in both biology and physics. For physicists, the cytoskeleton provides an exceptional toolbox to study materials far from equilibrium. For biologists, these studies will provide new understanding of how molecular-scale processes determine cell morphological changes. PMID:23112229

Physical chemistry: Molecular motion watched

NASA Astrophysics Data System (ADS)

Siwick, Bradley; Collet, Eric

2013-04-01

A laser pulse can switch certain crystals from an insulating phase to a highly conducting phase. The ultrafast molecular motions that drive the transition have been directly observed using electron diffraction. See Letter p.343

Applications of molecular physics 'biotechnology' to the rational design of an improved phenytoin analogue.

PubMed

Weaver, D F

1992-12-01

This study exploits molecular physics, in conjunction with a large scale computing environment, as a tool for understanding the clinical phenomenology of phenytoin (PHT) toxicology at a molecular level and for employing this understanding in an attempt to design improved drugs. The application of molecular physics techniques, such as quantum mechanics and molecular force field calculations, to the process of rational anticonvulsant drug design remains virtually unexplored. A 3-step strategy for applying these techniques to the design of an improved PHT molecule is presented. Step 1 employs quantitative structure-activity relationship calculations on 80 PHT analogues to ascertain the portion of the PHT molecule necessary for bioactivity (i.e. the 'bioactive face' of PHT); the N3-C4(O)-C5-R fragment of PHT was identified as the bioactive face. Step 2 employs molecular modelling studies to determine the portion of the PHT molecule necessary for the teratogenic, mutagenic and connective tissue toxicities of PHT (i.e. the 'biotoxic face'); the C2(O)-N3 fragment of PHT was identified as the biotoxic face. Step 3 experiments design an 'improved' PHT analogue, which maintains the bioactive face while eliminating the integrity of the biotoxic face; 2-deoxy-5,5-diphenylhydantoin was designed and synthesized as the improved PHT analogue. This compound had biological activity equivalent to PHT, but was unable to bind to nucleic acids or to chelate metals involved in connective tissue metabolism.

The effect of processing on the surface physical stability of amorphous solid dispersions.

PubMed

Yang, Ziyi; Nollenberger, Kathrin; Albers, Jessica; Moffat, Jonathan; Craig, Duncan; Qi, Sheng

2014-11-01

The focus of this study was to investigate the effect of processing on the surface crystallization of amorphous molecular dispersions and gain insight into the mechanisms underpinning this effect. The model systems, amorphous molecular dispersions of felodipine-EUDRAGIT® E PO, were processed both using spin coating (an ultra-fast solvent evaporation based method) and hot melt extrusion (HME) (a melting based method). Amorphous solid dispersions with drug loadings of 10-90% (w/w) were obtained by both processing methods. Samples were stored under 75% RH/room temperatures for up to 10months. Surface crystallization was observed shortly after preparation for the HME samples with high drug loadings (50-90%). Surface crystallization was characterized by powder X-ray diffraction (PXRD), ATR-FTIR spectroscopy and imaging techniques (SEM, AFM and localized thermal analysis). Spin coated molecular dispersions showed significantly higher surface physical stability than hot melt extruded samples. For both systems, the progress of the surface crystal growth followed zero order kinetics on aging. Drug enrichment at the surfaces of HME samples on aging was observed, which may contribute to surface crystallization of amorphous molecular dispersions. In conclusion it was found the amorphous molecular dispersions prepared by spin coating had a significantly higher surface physical stability than the corresponding HME samples, which may be attributed to the increased process-related apparent drug-polymer solubility and reduced molecular mobility due to the quenching effect caused by the rapid solvent evaporation in spin coating. Copyright © 2014 Elsevier B.V. All rights reserved.

Research Investigation Directed Toward Extending the Useful Range of the Electromagnetic Spectrum. [atomic spectra and electronic structure of alkali metals

NASA Technical Reports Server (NTRS)

Hartmann, S. R.; Happer, W.

1974-01-01

The report discusses completed and proposed research in atomic and molecular physics conducted at the Columbia Radiation Laboratory from July 1972 to June 1973. Central topics described include the atomic spectra and electronic structure of alkali metals and helium, molecular microwave spectroscopy, the resonance physics of photon echoes in some solid state systems (including Raman echoes, superradiance, and two photon absorption), and liquid helium superfluidity.

Crosslink Density and Molecular Weight Effects on the Viscoelastic Response of a Glassy High-Performance Polyimide

NASA Technical Reports Server (NTRS)

Nicholson, Lee M.; Whitley, Karen S.; Gates, Thomas S.

2001-01-01

Durability and long-term performance are among the primary concerns for the use of advanced polymer matrix composites (PMCs) in modern aerospace structural applications. For a PMC subJected to long-term exposure at elevated temperatures. the viscoelastic nature of the polymer matrix will contribute to macroscopic changes in composite stiffness, strength and fatigue life. Over time. changes in the polymer due to physical aging will have profound effects on tile viscoelastic compliance of the material, hence affecting its long-term durability. Thus, the ability to predict material performance using intrinsic properties, such as crosslink density and molecular weight, would greatly enhance the efficiency of design and development of PMCs. The objective of this paper is to discuss and present the results of an experimental study that considers the effects of crosslink density, molecular weight and temperature on the viscoelastic behavior including physical aging of an advanced polymer. Five distinct variations in crosslink density were used to evaluate the differences in mechanical performance of an advanced polyimide. The physical aging behavior was isolated by conducting sequenced, short-term isothermal creep compliance tests in tension. These tests were performed over a range of sub-glass transition temperatures. The material constants, material master curves and physical aging-related parameters were evaluated as a function of temperature crosslink density and molecular weight using time-temperature and time-aging time superposition techniques.

Mechanical design of DNA nanostructures

NASA Astrophysics Data System (ADS)

Castro, Carlos E.; Su, Hai-Jun; Marras, Alexander E.; Zhou, Lifeng; Johnson, Joshua

2015-03-01

Structural DNA nanotechnology is a rapidly emerging field that has demonstrated great potential for applications such as single molecule sensing, drug delivery, and templating molecular components. As the applications of DNA nanotechnology expand, a consideration of their mechanical behavior is becoming essential to understand how these structures will respond to physical interactions. This review considers three major avenues of recent progress in this area: (1) measuring and designing mechanical properties of DNA nanostructures, (2) designing complex nanostructures based on imposed mechanical stresses, and (3) designing and controlling structurally dynamic nanostructures. This work has laid the foundation for mechanically active nanomachines that can generate, transmit, and respond to physical cues in molecular systems.Structural DNA nanotechnology is a rapidly emerging field that has demonstrated great potential for applications such as single molecule sensing, drug delivery, and templating molecular components. As the applications of DNA nanotechnology expand, a consideration of their mechanical behavior is becoming essential to understand how these structures will respond to physical interactions. This review considers three major avenues of recent progress in this area: (1) measuring and designing mechanical properties of DNA nanostructures, (2) designing complex nanostructures based on imposed mechanical stresses, and (3) designing and controlling structurally dynamic nanostructures. This work has laid the foundation for mechanically active nanomachines that can generate, transmit, and respond to physical cues in molecular systems. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07153k

Conception and development of the Second Life® Embryo Physics Course.

PubMed

Gordon, Richard

2013-06-01

The study of embryos with the tools and mindset of physics, started by Wilhelm His in the 1880s, has resumed after a hiatus of a century. The Embryo Physics Course convenes online allowing interested researchers and students, who are scattered around the world, to gather weekly in one place, the virtual world of Second Life®. It attracts people from a wide variety of disciplines and walks of life: applied mathematics, artificial life, bioengineering, biophysics, cancer biology, cellular automata, civil engineering, computer science, embryology, electrical engineering, evolution, finite element methods, history of biology, human genetics, mathematics, molecular developmental biology, molecular biology, nanotechnology, philosophy of biology, phycology, physics, self-reproducing systems, stem cells, tensegrity structures, theoretical biology, and tissue engineering. Now in its fifth year, the Embryo Physics Course provides a focus for research on the central question of how an embryo builds itself.

3D Printing of Molecular Models

ERIC Educational Resources Information Center

Gardner, Adam; Olson, Arthur

2016-01-01

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

Molecular Astrophysics from Space: the Physical and Chemical Effects of Star Formation and the Destruction of Planetary Systems around Evolved Stars

NASA Technical Reports Server (NTRS)

Neufeld, David

2005-01-01

The research conducted during the reporting period is grouped into three sections: 1) Warm molecular gas in the interstellar medium (ISM); 2) Absorption line studies of "cold" molecular clouds; 3) Vaporization of comets around the AGB star IRC+10216.

Role of magnetic and diamagnetic interactions in molecular optics and scattering

NASA Astrophysics Data System (ADS)

Forbes, Kayn A.

2018-05-01

This paper aims to explicitly clarify the role and interpretation of diamagnetic interactions between molecules and light in quantum electrodynamics. In contrast to their electric and magnetic counterparts, the diamagnetic couplings between light and matter have received relatively little interest in the field of molecular optics. This intriguing disregard of an interaction term is puzzling. The diamagnetic couplings possess unique physical properties that warrant their inclusion in any multiphoton process, and the lack of gauge invariance for paramagnetic and diamagnetic susceptibilities necessitates their inclusion. Their role and importance within nonrelativistic molecular quantum electrodynamics in the Coulomb gauge is illuminated, and it is highlighted how for any multiphoton process their inclusion should be implicit. As an indicative example of the theory presented, the diamagnetic contributions to both forward and nonforward Rayleigh scattering are derived and put into context alongside the electric and magnetic molecular responses. The work represents clarification of diamagnetic couplings in molecular quantum electrodynamics, which subsequently should proffer the study of diamagnetic interactions in molecular optics due to their unique physical attributes and necessary inclusion in multiphoton processes.

Soft matter food physics--the physics of food and cooking.

PubMed

Vilgis, Thomas A

2015-12-01

This review discusses the (soft matter) physics of food. Although food is generally not considered as a typical model system for fundamental (soft matter) physics, a number of basic principles can be found in the interplay between the basic components of foods, water, oil/fat, proteins and carbohydrates. The review starts with the introduction and behavior of food-relevant molecules and discusses food-relevant properties and applications from their fundamental (multiscale) behavior. Typical food aspects from 'hard matter systems', such as chocolates or crystalline fats, to 'soft matter' in emulsions, dough, pasta and meat are covered and can be explained on a molecular basis. An important conclusion is the point that the macroscopic properties and the perception are defined by the molecular interplay on all length and time scales.

Numerical studies from quantum to macroscopic scales of carbon nanoparticules in hydrogen plasma

NASA Astrophysics Data System (ADS)

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

2016-09-01

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

Electronic effects and fundamental physics studied in molecular interfaces.

PubMed

Pope, Thomas; Du, Shixuan; Gao, Hong-Jun; Hofer, Werner A

2018-05-29

Scanning probe instruments in conjunction with a very low temperature environment have revolutionized the ability of building, functionalizing, and analysing two dimensional interfaces in the last twenty years. In addition, the availability of fast, reliable, and increasingly sophisticated methods to simulate the structure and dynamics of these interfaces allow us to capture even very small effects at the atomic and molecular level. In this review we shall focus largely on metal surfaces and organic molecular compounds and show that building systems from the bottom up and controlling the physical properties of such systems is no longer within the realm of the desirable, but has become day to day reality in our best laboratories.

Production of high molecular weight polylactic acid

DOEpatents

Bonsignore, P.V.

1995-11-28

A degradable high molecular weight poly(lactic acid) is described. The poly(lactic acid) has a terminal end group of one of carboxyl or hydroxyl groups with low molecular weight poly(lactic acid) units coupled with linking agents of di-isocyanates, bis-epoxides, bis-oxazolines and bis-ortho esters. The resulting high molecular weight poly(lactic acid) can be used for applications taking advantage of the improved physical properties.

Dr. Steven Chu, Secretary of Energy

Science.gov Websites

Molecular and Cell Biology at the University of California. He successfully applied the techniques he developed in atomic physics to molecular biology, and since 2004, motivated by his deep interest in climate

The TensorMol-0.1 model chemistry: a neural network augmented with long-range physics.

PubMed

Yao, Kun; Herr, John E; Toth, David W; Mckintyre, Ryker; Parkhill, John

2018-02-28

Traditional force fields cannot model chemical reactivity, and suffer from low generality without re-fitting. Neural network potentials promise to address these problems, offering energies and forces with near ab initio accuracy at low cost. However a data-driven approach is naturally inefficient for long-range interatomic forces that have simple physical formulas. In this manuscript we construct a hybrid model chemistry consisting of a nearsighted neural network potential with screened long-range electrostatic and van der Waals physics. This trained potential, simply dubbed "TensorMol-0.1", is offered in an open-source Python package capable of many of the simulation types commonly used to study chemistry: geometry optimizations, harmonic spectra, open or periodic molecular dynamics, Monte Carlo, and nudged elastic band calculations. We describe the robustness and speed of the package, demonstrating its millihartree accuracy and scalability to tens-of-thousands of atoms on ordinary laptops. We demonstrate the performance of the model by reproducing vibrational spectra, and simulating the molecular dynamics of a protein. Our comparisons with electronic structure theory and experimental data demonstrate that neural network molecular dynamics is poised to become an important tool for molecular simulation, lowering the resource barrier to simulating chemistry.

Some Thermodynamic Considerations on the Physical and Quantum Nature of Space and Time

NASA Technical Reports Server (NTRS)

Sohrab, Siavash H.; Piltch, Nancy (Technical Monitor)

2000-01-01

It is suggested that the Planck h = m(sub k)c Lambda(sub k) and the Boltzmann k = m(sub k)c nu(sub k)Constants have stochastic foundation. It is further suggested that a body of fluid at equilibrium is composed of a spectrum of molecular clusters (energy levels) the size of which are governed by the Maxwell-Boltzmann distribution function. Brownian motions are attributed to equilibrium between suspensions and molecular clusters. Atomic (molecular) transition between different size atomic- (molecular-) clusters (energy levels) is shown to result in emission/absorption of energy in accordance with Bohr's theory of atomic spectra. Physical space is identified as a tachyonic fluid that is Dirac's stochastic ether or de Broglie's hidden thermostat. Compressibility of physical space, in accordance with Planck's compressible ether, is shown to result in the Lorentz-Fitzgerald contraction, thus providing a causal explanation of relativistic effect in accordance with the perceptions of Poincare and Lorentz. The invariant Schrodinger equation is derived from the invariant Bernoulli equation for incompressible potential flow. Following Heisenberg a temporal uncertainty relation is introduced as Delta(nu(sub Beta)) Delta(Rho(sub Beta)) > = k.

The equally wonderful field: Ernst Mayr and organismic biology.

PubMed

Milam, Erika Lorraine

2010-01-01

Biologists in the 1960s witnessed a period of intense intra-disciplinary negotiations, especially the positioning of organismic biologists relative to molecular biologists. The perceived valorization of the physical sciences by "molecular" biologists became a catalyst creating a unified front of "organismic" biology that incorporated not just evolutionary biologists, but also students of animal behavior, ecology, systematics, botany - in short, almost any biological community that predominantly conducted their research in the field or museum and whose practitioners felt the pinch of the prestige and funding accruing to molecular biologists and biochemists. Ernst Mayr, Theodosius Dobzhansky, and George Gaylord Simpson took leading roles in defending alternatives to what they categorized as the mechanistic approach of chemistry and physics applied to living systems - the "equally wonderful field of organismic biology." Thus, it was through increasingly tense relations with molecular biology that organismic biologists cohered into a distinct community, with their own philosophical grounding, institutional security, and historical identity. Because this identity was based in large part on a fundamental rejection of the physical sciences as a desirable model within biology, organismic biologists succeeded in protecting the future of their field by emphasizing deep divisions that ran through the biological sciences as a whole.

The Interface between Physics and Biology: An Unexplored Territory.

ERIC Educational Resources Information Center

Marx, George

1980-01-01

Discusses from the physicist's point of view the connection between biology and physics and the usefulness of physical laws for understanding biological processes. Discusses these fields of research in secondary school science: molecular science, regulation, statistics and information, corrosion and evolution, chance and necessity, and…

Molecular-level Analysis of Shock-wave Physics and Derivation of the Hugoniot Relations for Soda-lime Glass

DTIC Science & Technology

2011-06-17

based glasses like fused silica and soda - lime glass , the polyhedral central cation is silicon. In this case, each silicon is surrounded by four oxygen...to two network forming cations) oxygen atoms per network polyhedron. The equilibrium values for this parameter in fused silica and soda - lime glass ...Molecular-level analysis of shock-wave physics and derivation of the Hugoniot relations for soda - lime glass M. Grujicic • B. Pandurangan • W. C. Bell

Low-molecular-weight heparins: differential characterization/physical characterization.

PubMed

Guerrini, Marco; Bisio, Antonella

2012-01-01

Low-molecular-weight heparins (LMWHs), derived from unfractionated heparin (UFH) through different depolymerization processes, have advantages with respect to the parent heparin in terms of pharmacokinetics, convenience of administration, and reduced side effects. Each LMWH can be considered as an independent drug with its own activity profile, placing significance on their biophysical characterization, which will also enable a better understanding of their structure-function relationship. Several chemical and physical methods, some involving sample modification, are now available and are reviewed.

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

Elber, Ron

Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances.

Developing model asphalt systems using molecular simulation : final model.

DOT National Transportation Integrated Search

2009-09-01

Computer based molecular simulations have been used towards developing simple mixture compositions whose : physical properties resemble those of real asphalts. First, Monte Carlo simulations with the OPLS all-atom force : field were used to predict t...

| NREL

Science.gov Websites

of NREL's Computational Science Center, where he uses electronic structure calculations and other introductory chemistry and physical chemistry. Research Interests Electronic structure and dynamics in the quantum/classical molecular dynamics simulation|Coupling of molecular electronic structure to

The Physics of Molecular Shocks in Star-Forming Regions

NASA Technical Reports Server (NTRS)

Hollenbach, David; Cuzzi, Jeffrey (Technical Monitor)

1996-01-01

Molecular shocks are produced by the impact of the supersonic infall of gas and dust onto protostars and by the interaction of the supersonic outflow from the protostar with the circumstellar material. Infalling gas creates an accretion shock around the circumstellar disk which emits a unique infrared spectrum and which processes the interstellar dust as it enters the disk. The winds and jets from protostars also impact the disk, the infalling material, and the ambient molecular cloud core creating shocks whose spectrum and morphology diagnose the mass loss processes of the protostar and the orientation and structure of the star forming system. We discuss the physics of these shocks, the model spectra derived from theoretical models, and comparisons with observations of H2O masers, H2 emission, as well as other shocks tracers. We show the strong effect of magnetic fields on molecular shock structure, and elucidate the chemical changes induced by the shock heating and compression.

The cognitive life of mechanical molecular models.

PubMed

Charbonneau, Mathieu

2013-12-01

The use of physical models of molecular structures as research tools has been central to the development of biochemistry and molecular biology. Intriguingly, it has received little attention from scholars of science. In this paper, I argue that these physical models are not mere three-dimensional representations but that they are in fact very special research tools: they are cognitive augmentations. Despite the fact that they are external props, these models serve as cognitive tools that augment and extend the modeler's cognitive capacities and performance in molecular modeling tasks. This cognitive enhancement is obtained because of the way the modeler interacts with these models, the models' materiality contributing to the solving of the molecule's structure. Furthermore, I argue that these material models and their component parts were designed, built and used specifically to serve as cognitive facilitators and cognitive augmentations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Delocalized electrons in atomic and molecular nanoclusters

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

Kresin, Vitaly

The aim of the award (Program director: Dr. Mark Pederson) was to facilitate the attendance of researchers, students, and postdocs from the U.S. at the international workshop co-organized by the applicant. The award succeeded in making it possible for a number of US attendees to present their work and participate in the meeting, which was a significant event in the research community at the interdisciplinary interface of physical chemistry, nanoscience, atomic and molecular physics, condensed matter physics, and spectroscopy. The workshop did not issue proceedings, but the present report includes present the schedule, the abstracts, and the attendance list ofmore » the July 2016 Workshop. DOE sponsorship is gratefully acknowledged in the program.« less

Kinetic Theory and Simulation of Single-Channel Water Transport

NASA Astrophysics Data System (ADS)

Tajkhorshid, Emad; Zhu, Fangqiang; Schulten, Klaus

Water translocation between various compartments of a system is a fundamental process in biology of all living cells and in a wide variety of technological problems. The process is of interest in different fields of physiology, physical chemistry, and physics, and many scientists have tried to describe the process through physical models. Owing to advances in computer simulation of molecular processes at an atomic level, water transport has been studied in a variety of molecular systems ranging from biological water channels to artificial nanotubes. While simulations have successfully described various kinetic aspects of water transport, offering a simple, unified model to describe trans-channel translocation of water turned out to be a nontrivial task.

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

Stelson, P.H.

The bulk of the Division's effort concerned nuclear physics and accelerator development, but work in the areas of nuclear data, research applicable to the magnetic fusion project, atomic and molecular physics, and high-energy physics is also recounted. Lists of publications, technical talks, personnel, etc., are included. Individual reports with sufficient data are abstracted separately. (RWR)

75 Easy Physics Demonstrations. Teacher Book.

ERIC Educational Resources Information Center

Kardos, Thomas

This book is a collection of classroom demonstrations in physics designed to present basic scientific ideas on a concrete level. The topics covered include: physical change and properties of matter; energy waves and energy forms; absorption of heat; radiant energy; vacuum bottles; kinetic molecular theory; states of matter; pressure of air; work…

The physics of life: one molecule at a time

PubMed Central

Leake, Mark C.

2013-01-01

The esteemed physicist Erwin Schrödinger, whose name is associated with the most notorious equation of quantum mechanics, also wrote a brief essay entitled ‘What is Life?’, asking: ‘How can the events in space and time which take place within the spatial boundary of a living organism be accounted for by physics and chemistry?’ The 60+ years following this seminal work have seen enormous developments in our understanding of biology on the molecular scale, with physics playing a key role in solving many central problems through the development and application of new physical science techniques, biophysical analysis and rigorous intellectual insight. The early days of single-molecule biophysics research was centred around molecular motors and biopolymers, largely divorced from a real physiological context. The new generation of single-molecule bioscience investigations has much greater scope, involving robust methods for understanding molecular-level details of the most fundamental biological processes in far more realistic, and technically challenging, physiological contexts, emerging into a new field of ‘single-molecule cellular biophysics’. Here, I outline how this new field has evolved, discuss the key active areas of current research and speculate on where this may all lead in the near future. PMID:23267186

Exploring parameter space effects on structure-property relationships of surfactants at liquid-liquid interfaces.

PubMed

Emborsky, Christopher P; Cox, Kenneth R; Chapman, Walter G

2011-08-28

The ubiquitous use of surfactants in commercial and industrial applications has led to many experimental, theoretical, and simulation based studies. These efforts seek to provide a molecular level understanding of the effects on structuring behavior and the corresponding impacts on observable properties (e.g., interfacial tension). With such physical detail, targeted system design can be improved over typical techniques of observational trends and phenomenological correlations by taking advantage of predictive system response. This research provides a systematic study of part of the broad parameter space effects on equilibrium microstructure and interfacial properties of amphiphiles at a liquid-liquid interface using the interfacial statistical associating fluid theory density functional theory as a molecular model for the system from the bulk to the interface. Insights into the molecular level physics and thermodynamics governing the system behavior are discussed as they relate to both predictions qualitatively consistent with experimental observations and extensions beyond currently available studies. © 2011 American Institute of Physics

Classroom Demonstrations of Polymer Principles. Part III. Physical States and Transitions.

ERIC Educational Resources Information Center

Rodriguez, F.; And Others

1988-01-01

Presented is a classification of polymers according to physical condition. Considered are molecular structure and arrangements. Described are demonstrations using polarized light and the mechanical properties of polymers. (CW)

Running from Disease: Molecular Mechanisms Associating Dopamine and Leptin Signaling in the Brain with Physical Inactivity, Obesity, and Type 2 Diabetes.

PubMed

Ruegsegger, Gregory N; Booth, Frank W

2017-01-01

Physical inactivity is a primary contributor to diseases such as obesity, cardiovascular disease, and type 2 diabetes. Accelerometry data suggest that a majority of US adults fail to perform substantial levels of physical activity needed to improve health. Thus, understanding the molecular factors that stimulate physical activity, and physical inactivity, is imperative for the development of strategies to reduce sedentary behavior and in turn prevent chronic disease. Despite many of the well-known health benefits of physical activity being described, little is known about genetic and biological factors that may influence this complex behavior. The mesolimbic dopamine system regulates motivating and rewarding behavior as well as motor movement. Here, we present data supporting the hypothesis that obesity may mechanistically lower voluntary physical activity levels via dopamine dysregulation. In doing so, we review data that suggest mesolimbic dopamine activity is a strong contributor to voluntary physical activity behavior. We also summarize findings suggesting that obesity leads to central dopaminergic dysfunction, which in turn contributes to reductions in physical activity that often accompany obesity. Additionally, we highlight examples in which central leptin activity influences physical activity levels in a dopamine-dependent manner. Future elucidation of these mechanisms will help support strategies to increase physical activity levels in obese patients and prevent diseases caused by physical inactivity.

An evaluation of the effects of PEO/PEG molecular weights on extruded alumina rods

NASA Astrophysics Data System (ADS)

Bolger, Nancy Beth

1998-12-01

Alumina rods were piston extruded from bodies containing polyethylene glycols (PEGs) and polyethylene oxides (PEOs) with molecular weights ranging from 1,300 to 3,800,000 g/mol. A blend of aluminas possessing different particle size distributions was evaluated with regard to its extrusion pressure by varying the amount of PEG/PEO addition. Behavior exhibited by the alumina blend was dependent upon the additive that was used. The higher molecular weight binders with average molecular weight of 200,000 g/mol and 3,350,000 g/mol displayed the most severe behaviors of near dilatant and dilatant respectively. Physical properties of the green and fired states, as well as the binder burnout, were investigated with the changing additions. Correlation between the green and fired strengths and the changing molecular weights were examined. The additive present influenced the surface properties of the rods, which affected the green strengths. The highest average molecular weight polyethylene glycols showed higher green strengths, while the lowest green strengths were observed for the high molecular weight polyethylene oxides. Fired strengths generally ranged from approximately 12,000 psi to 16,000 psi for additive batches. Alumina pellets containing twelve separate combinations of polyethylene glycol with polyethylene oxide were dry pressed. Physical properties of the green and fired states were examined. Statistical analysis was performed upon the data and seven combinations of polyethylene glycol with polyethylene oxide were deemed significant. These combinations in conjunction with the same alumina blend were then piston extruded. The addition of polyethylene glycol reduced the near dilatant behavior exhibited by the 200,000 g/mol average molecular weight polyethylene oxide. Dilatant behavior was completely eliminated from the 3,350,000 g/mol average molecular weight polyethylene oxide batches. Physical properties of the green and fired states were again investigated with the changing additions. Polyethylene oxide, in combination with polyethylene glycol, did show an increase in green strength versus the polyethylene oxide alone. Strengths were still lower than those displayed by the polyethylene glycols alone. Reductions or degradations in molecular weight of the polymers due to mixing and extrusion processes may account for lower green strength of bodies, especially those containing polyethylene oxides.

Masses, luminosities and dynamics of galactic molecular clouds

NASA Technical Reports Server (NTRS)

Solomon, P. M.; Rivolo, A. R.; Mooney, T. J.; Barrett, J. W.; Sage, L. J.

1987-01-01

Star formation in galaxies takes place in molecular clouds and the Milky Way is the only galaxy in which it is possible to resolve and study the physical properties and star formation activity of individual clouds. The masses, luminosities, dynamics, and distribution of molecular clouds, primarily giant molecular clouds in the Milky Way are described and analyzed. The observational data sets are the Massachusetts-Stony Brook CO Galactic Plane Survey and the IRAS far IR images. The molecular mass and infrared luminosities of glactic clouds are then compared with the molecular mass and infrared luminosities of external galaxies.

Trapped ultracold molecular ions: candidates for an optical molecular clock for a fundamental physics mission in space

NASA Astrophysics Data System (ADS)

Roth, B.; Koelemeij, J.; Daerr, H.; Ernsting, I.; Jorgensen, S.; Okhapkin, M.; Wicht, A.; Nevsky, A.; Schiller, S.

2017-11-01

Narrow ro-vibrational transitions in ultracold molecules are excellent candidates for frequency references in the near-IR to visible spectral domain and interesting systems for fundamental tests of physics, in particular for a satellite test of the gravitational redshift of clocks. We have performed laser spectroscopy of several ro-vibrational overtone transitions υ = 0 → υ = 4 in HD+ ions at around 1.4 μm. 1+1 REMPD was used as a detection method, followed by measurement of the number of remaining molecules. The molecular ions were stored in a linear radiofrequency trap and cooled to millikelvin temperatures, by sympathetic cooling using laser-cooled Be+ ions simultaneously stored in the same trap.

The Transition from Mathematician to Astrophysicist

NASA Astrophysics Data System (ADS)

Flannery, M. R.

Various landmarks in the evolution of Alexander Dalgarno from a gifted mathematician to becoming the acknowledged Father of Molecular Astrophysics are noted. His researches in basic atomic and molecular physics, aeronomy (the study of the upper atmosphere) and astrophysics are highlighted.

Interrogating selectivity in catalysis using molecular vibrations

NASA Astrophysics Data System (ADS)

Milo, Anat; Bess, Elizabeth N.; Sigman, Matthew S.

2014-03-01

The delineation of molecular properties that underlie reactivity and selectivity is at the core of physical organic chemistry, and this knowledge can be used to inform the design of improved synthetic methods or identify new chemical transformations. For this reason, the mathematical representation of properties affecting reactivity and selectivity trends, that is, molecular parameters, is paramount. Correlations produced by equating these molecular parameters with experimental outcomes are often defined as free-energy relationships and can be used to evaluate the origin of selectivity and to generate new, experimentally testable hypotheses. The premise behind successful correlations of this type is that a systematically perturbed molecular property affects a transition-state interaction between the catalyst, substrate and any reaction components involved in the determination of selectivity. Classic physical organic molecular descriptors, such as Hammett, Taft or Charton parameters, seek to independently probe isolated electronic or steric effects. However, these parameters cannot address simultaneous, non-additive variations to more than one molecular property, which limits their utility. Here we report a parameter system based on the vibrational response of a molecule to infrared radiation that can be used to mathematically model and predict selectivity trends for reactions with interlinked steric and electronic effects at positions of interest. The disclosed parameter system is mechanistically derived and should find broad use in the study of chemical and biological systems.

Molecular aspects of magnetic resonance imaging and spectroscopy.

PubMed

Boesch, C

1999-01-01

Magnetic resonance imaging (MRI) is a well known diagnostic tool in radiology that produces unsurpassed images of the human body, in particular of soft tissue. However, the medical community is often not aware that MRI is an important yet limited segment of magnetic resonance (MR) or nuclear magnetic resonance (NMR) as this method is called in basic science. The tremendous morphological information of MR images sometimes conceal the fact that MR signals in general contain much more information, especially on processes on the molecular level. NMR is successfully used in physics, chemistry, and biology to explore and characterize chemical reactions, molecular conformations, biochemical pathways, solid state material, and many other applications that elucidate invisible characteristics of matter and tissue. In medical applications, knowledge of the molecular background of MRI and in particular MR spectroscopy (MRS) is an inevitable basis to understand molecular phenomenon leading to macroscopic effects visible in diagnostic images or spectra. This review shall provide the necessary background to comprehend molecular aspects of magnetic resonance applications in medicine. An introduction into the physical basics aims at an understanding of some of the molecular mechanisms without extended mathematical treatment. The MR typical terminology is explained such that reading of original MR publications could be facilitated for non-MR experts. Applications in MRI and MRS are intended to illustrate the consequences of molecular effects on images and spectra.

A physical feast

NASA Astrophysics Data System (ADS)

Harris, Margaret

2016-08-01

With its penchant for using centrifuges, water baths and other laboratory tools to whip up novel tastes and textures, modernist cuisine - also known as “molecular gastronomy” - has a reputation for complexity. In his book Molecular Gastronomy at Home, chef Jozef Youssef aims to change that.

Glauber-theory approach for molecular vibrational excitations

NASA Technical Reports Server (NTRS)

Chang, T. N.; Poe, R. T.; Ray, P.

1973-01-01

Molecular vibrational excitations by charged-particle impact are investigated within the Glauber-theory approach. Theoretical results for electron-H2 scattering give good agreement with experimental data. We study the physical effects responsible for the structures in the differential cross section.

A Course in Biophysics: An Integration of Physics, Chemistry, and Biology

ERIC Educational Resources Information Center

Giancoli, Douglas C.

1971-01-01

Describes an interdisciplinary course for advanced undergraduates in the physical and biological sciences. The goal is to understand a living cell from the most basic standpoint possible. The ideas of physics, chemistry, and molecular biology are all essential to the course, which leads to a unified view of the sciences. (PR)

US Navy FY 1997 Research Program

DTIC Science & Technology

1997-09-30

US NAVY FY 1997 RESEARCH PROGRAM Henry E. Bass National Center for Physical Acoustics University of Mississippi University, MS 38677 Phone: (601...232-5905 Fax: (601) 232-7494 Email: pabass@olemiss.edu Award Number: N00014-95-1-1306 LONG-TERM GOALS The National Center for Physical Acoustics ...NCPA) provides an integrated physical acoustics laboratory to facilitate research in sound propagation and attenuation, molecular and chemical physics

Bose-Einstein Condensates in 1D Optical Lattices: Nonlinearity and Wannier-Stark Spectra

NASA Astrophysics Data System (ADS)

Arimondo, Ennio; Ciampini, Donatella; Morsch, Oliver

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

Chitosan in Molecularly-Imprinted Polymers: Current and Future Prospects.

PubMed

Xu, Long; Huang, Yun-An; Zhu, Qiu-Jin; Ye, Chun

2015-08-07

Chitosan is widely used in molecular imprinting technology (MIT) as a functional monomer or supporting matrix because of its low cost and high contents of amino and hydroxyl functional groups. The various excellent properties of chitosan, which include nontoxicity, biodegradability, biocompatibility, and attractive physical and mechanical performances, make chitosan a promising alternative to conventional functional monomers. Recently, chitosan molecularly-imprinted polymers have gained considerable attention and showed significant potential in many fields, such as curbing environmental pollution, medicine, protein separation and identification, and chiral-compound separation. These extensive applications are due to the polymers' desired selectivity, physical robustness, and thermal stability, as well as their low cost and easy preparation. Cross-linkers, which fix the functional groups of chitosan around imprinted molecules, play an important role in chitosan molecularly-imprinted polymers. This review summarizes the important cross-linkers of chitosan molecularly-imprinted polymers and illustrates the cross-linking mechanism of chitosan and cross-linkers based on the two glucosamine units. Finally, some significant attempts to further develop the application of chitosan in MIT are proposed.

[Stability of physical state on compound hawthorn dropping pills].

PubMed

Zhang, Wei; Chen, Hong-Yan; Jiang, Jian-Lan

2008-11-01

To evaluate the stability of physical state with accelerate test and dropping in process before and after on compound hawthorn dropping pills. Scanning electron microscope, TG-DTA, FT-IR and XRD were used. The active components presented amorphous, tiny crystal and molecular state in dropping pills, and it had no obvious reaction between PEG 4000 and active components. With time prolonging, a little of active components changed from amorphous state to tiny crystal or molecular state. Solid dispersion improved the stability and dissolution of compound hawthorn dropping pills.

Fast Outflow of Molecular Gas in the Seyfert Galaxy IC 5063

NASA Astrophysics Data System (ADS)

Morganti, Raffaella; Oosterloo, T.; Oonk, R.; Tadhunter, C.

2017-11-01

AGN-driven gas outflows may play an important role in the evolution of galaxies, as they impact on the growth on the central supermassive black hole as well on the star formation of the host galaxy. Much of the detailed physics of these gas outflows, and their actual impact on the host galaxy, is still not well understood. We present a detailed analysis, using ALMA observations, of the radio-jet driven outflow of molecular gas in the nearby radio-loud Seyfert galaxy IC 5063 which allows to derive important physical parameters of the gas and the outflow which, in turn, provide crucial input to numerical models. In recent years, a surprising result in the field of AGN-driven outflows has been that the cold phases of the gas (atomic and molecular) in some galaxies are the massive components of these outflows, despite the huge amounts of energy involved in driving these outflows. However, why most of the outflowing gas should be molecular/atomic, and in general, what are the physical conditions of the gas in the outflows and what really drives them, are still open questions. We present the results obtained from ALMA observations of multiple CO transitions and other molecules of what appears to be a textbook case of a jet-driven multi- phase outflow in the central regions of the Seyfert galaxy IC 5063. The data on multiple transitions allow us to derive the physical conditions in the different regions of the outflowing molecular gas. The signature of the impact of the radio jet is clearly seen in the spatial distribution of the excitation temperature and pressure of the outflowing gas, with the highest excitation and pressure found for the gas with the highest outflow velocities. We obtain a detailed three- dimensional picture of the outflow, and its kinematics, and find that outflowing molecular gas is present across the entire region co-spatial with the radio plasma, providing unambiguous evidence that the radio jets/cocoon are responsible for the outflow. The detailed information about the physical condition of the gas in a fast outflow will serve as template for the signatures of the impact of a radio plasma jet on a gas-rich ISM and its associated star formation, and guide the studies of outflows in other galaxies, including higher redshift objects.

Tracking and Motion Analysis of Crack Propagations in Crystals for Molecular Dynamics

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

Tsap, L V; Duchaineau, M; Goldgof, D B

2001-05-14

This paper presents a quantitative analysis for a discovery in molecular dynamics. Recent simulations have shown that velocities of crack propagations in crystals under certain conditions can become supersonic, which is contrary to classical physics. In this research, they present a framework for tracking and motion analysis of crack propagations in crystals. It includes line segment extraction based on Canny edge maps, feature selection based on physical properties, and subsequent tracking of primary and secondary wavefronts. This tracking is completely automated; it runs in real time on three 834-image sequences using forty 250 MHZ processors. Results supporting physical observations aremore » presented in terms of both feature tracking and velocity analysis.« less

Synthesis and characterization of star-shaped oligo(ethylene glycol) with tyrosine derived moieties under variation of their molecular weight.

PubMed

Julich-Gruner, Konstanze K; Roch, Toralf; Ma, Nan; Neffe, Axel T; Lendlein, Andreas

2015-01-01

Desamino tyrosine (DAT) and desamino tyrosyl tyrosine (DATT) can be used to functionalize the end groups of water soluble polymers. The phenolic groups may enable physical interactions by π- π interaction and hydrogen bonds, which might lead to the formation of a hydrogel by physical crosslinking. However, using star-shaped oligo(ethylene glycols) (sOEG) with a molecular weight of 5 kDa for functionalization with DAT or DATT resulted in the formation of surfactants and not in hydrogels.As the molecular weight of the sOEG polymer chain can have an influence on forming physical cross links, DAT(T)-fuctionalization of sOEGs with higher molecular weight was investigated, the polymers were structurally characterized and for their mechanical properties were evaluated by rheological measurements.Aqueous solutions of DAT(T)-sOEGs with 10 and 20 kDa showed lower storage and loss moduli compared to unfunctionalized sOEGs indicating also the formation of surfactants. Cell-based assays showed that all sOEG solutions did not impair cell viability and were free of endotoxins, which could otherwise induce uncontrolled immune responses.Conclusively, our data suggested that the sOEG solutions have surface active properties without inducing unwanted cellular responses, which is required e.g. in pharmaceutical applications to solubilize hydophobic substances.

Bringing physics to bear on the phenomenon of life: the divergent positions of Bohr, Delbrück, and Schrödinger.

PubMed

Domondon, Andrew T

2006-09-01

The received view on the contributions of the physics community to the birth of molecular biology tends to present the physics community as sharing a basic level consensus on how physics should be brought to bear on biology. I argue, however, that a close examination of the views of three leading physicists involved in the birth of molecular biology, Bohr, Delbrück, and Schrödinger, suggests that there existed fundamental disagreements on how physics should be employed to solve problems in biology even within the physics community. In particular, I focus on how these three figures differed sharply in their assessment of the relevance of complementarity, the potential of chemical methods, and the relative importance of classical physics. In addition, I assess and develop Roll-Hansen's attempt to conceptualize this history in terms of models of scientific change advanced by Kuhn and Lakatos. Though neither model is fully successful in explaining the divergence of views among these three physicists, I argue that the extent and quality of difference in their views help elucidate and extend some themes that are left opaque in Kuhn's model.

Limiting assumptions in molecular modeling: electrostatics.

PubMed

Marshall, Garland R

2013-02-01

Molecular mechanics attempts to represent intermolecular interactions in terms of classical physics. Initial efforts assumed a point charge located at the atom center and coulombic interactions. It is been recognized over multiple decades that simply representing electrostatics with a charge on each atom failed to reproduce the electrostatic potential surrounding a molecule as estimated by quantum mechanics. Molecular orbitals are not spherically symmetrical, an implicit assumption of monopole electrostatics. This perspective reviews recent evidence that requires use of multipole electrostatics and polarizability in molecular modeling.

MOLECULAR THERMODYNAMICS IN THE DESIGN OF SUBSTITUTE SOLVENTS

EPA Science Inventory

The use of physical properties and fluid behavior from molecular thermodynamics can lead to better decision making in the design of substitute solvents and can greatly reduce the expense and time required to find substitutes compared to designing solvents by experiment. this pape...

Turbulence in molecular clouds - A new diagnostic tool to probe their origin

NASA Technical Reports Server (NTRS)

Canuto, V. M.; Battaglia, A.

1985-01-01

A method is presented to uncover the instability responsible for the type of turbulence observed in molecular clouds and the value of the physical parameters of the 'placental medium' from which turbulence originated. The method utilizes the observational relation between velocities and sizes of molecular clouds, together with a recent model for large-scale turbulence (constructed by Canuto and Goldman, 1985).

Molecular Dynamics Characterization of the Conformational Landscape of Small Peptides: A Series of Hands-On Collaborative Practical Sessions for Undergraduate Students

ERIC Educational Resources Information Center

Rodrigues, João P. G. L. M.; Melquiond, Adrien S. J.; Bonvin, Alexandre M. J. J.

2016-01-01

Molecular modelling and simulations are nowadays an integral part of research in areas ranging from physics to chemistry to structural biology, as well as pharmaceutical drug design. This popularity is due to the development of high-performance hardware and of accurate and efficient molecular mechanics algorithms by the scientific community. These…

Molecular Structure and Sequence in Complex Coacervates

NASA Astrophysics Data System (ADS)

Sing, Charles; Lytle, Tyler; Madinya, Jason; Radhakrishna, Mithun

Oppositely-charged polyelectrolytes in aqueous solution can undergo associative phase separation, in a process known as complex coacervation. This results in a polyelectrolyte-dense phase (coacervate) and polyelectrolyte-dilute phase (supernatant). There remain challenges in understanding this process, despite a long history in polymer physics. We use Monte Carlo simulation to demonstrate that molecular features (charge spacing, size) play a crucial role in governing the equilibrium in coacervates. We show how these molecular features give rise to strong monomer sequence effects, due to a combination of counterion condensation and correlation effects. We distinguish between structural and sequence-based correlations, which can be designed to tune the phase diagram of coacervation. Sequence effects further inform the physical understanding of coacervation, and provide the basis for new coacervation models that take monomer-level features into account.

Hard Sphere Simulation by Event-Driven Molecular Dynamics: Breakthrough, Numerical Difficulty, and Overcoming the issues

NASA Astrophysics Data System (ADS)

Isobe, Masaharu

Hard sphere/disk systems are among the simplest models and have been used to address numerous fundamental problems in the field of statistical physics. The pioneering numerical works on the solid-fluid phase transition based on Monte Carlo (MC) and molecular dynamics (MD) methods published in 1957 represent historical milestones, which have had a significant influence on the development of computer algorithms and novel tools to obtain physical insights. This chapter addresses the works of Alder's breakthrough regarding hard sphere/disk simulation: (i) event-driven molecular dynamics, (ii) long-time tail, (iii) molasses tail, and (iv) two-dimensional melting/crystallization. From a numerical viewpoint, there are serious issues that must be overcome for further breakthrough. Here, we present a brief review of recent progress in this area.

QSPR models for various physical properties of carbohydrates based on molecular mechanics and quantum chemical calculations.

PubMed

Dyekjaer, Jane Dannow; Jónsdóttir, Svava Osk

2004-01-22

Quantitative Structure-Property Relationships (QSPR) have been developed for a series of monosaccharides, including the physical properties of partial molar heat capacity, heat of solution, melting point, heat of fusion, glass-transition temperature, and solid state density. The models were based on molecular descriptors obtained from molecular mechanics and quantum chemical calculations, combined with other types of descriptors. Saccharides exhibit a large degree of conformational flexibility, therefore a methodology for selecting the energetically most favorable conformers has been developed, and was used for the development of the QSPR models. In most cases good correlations were obtained for monosaccharides. For five of the properties predictions were made for disaccharides, and the predicted values for the partial molar heat capacities were in excellent agreement with experimental values.

Meeting moved due to discriminatory law

NASA Astrophysics Data System (ADS)

Kruesi, Liz

2016-09-01

The American Physical Society (APS) has relocated the 2018 annual meeting of the Division of Atomic, Molecular and Optical Physics (DAMOP) over concerns about a new state law that discriminates against members of the lesbian, gay, bisexual and transgender (LGBT) community.

REVIEWS OF TOPICAL PROBLEMS: Physical aspects of cryobiology

NASA Astrophysics Data System (ADS)

Zhmakin, A. I.

2008-03-01

Physical phenomena during biological freezing and thawing processes at the molecular, cellular, tissue, and organ levels are examined. The basics of cryosurgery and cryopreservation of cells and tissues are presented. Existing cryobiological models, including numerical ones, are reviewed.

Quantum Dots: An Experiment for Physical or Materials Chemistry

ERIC Educational Resources Information Center

Winkler, L. D.; Arceo, J. F.; Hughes, W. C.; DeGraff, B. A.; Augustine, B. H.

2005-01-01

An experiment is conducted for obtaining quantum dots for physical or materials chemistry. This experiment serves to both reinforce the basic concept of quantum confinement and providing a useful bridge between the molecular and solid-state world.

ESTIMATION OF PHYSICAL PROPERTIES AND CHEMICAL REACTIVITY PARAMETERS OF ORGANIC COMPOUNDS

EPA Science Inventory

The computer program SPARC (Sparc Performs Automated Reasoning in Chemistry)has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms ...

Nikolay Kirov Nikolov

NASA Astrophysics Data System (ADS)

Petrov, Minko; Reynolds, Steve

2014-12-01

Professor Nikolay Kirov Nikolov graduated in Chemistry from Sofia University 'St. Kliment Ohridski', Bulgaria, in 1968. He received his Ph.D. degree in 1973, D.Sc. in 1988 and was appointed to the position of Professor of Physics in the Institute of Solid State Physics (ISSP), Bulgarian Academy of Sciences (BAS), in 1989. Prof. Kirov rose to become an international authority in the area of molecular spectroscopy, and in particular in the vibrational spectroscopy of thermotropic liquid crystals. Prof. Kirov was a scientist of high reputation both in Bulgaria and globally. His scientific papers, numbering some 150, focus on the physics of liquid crystals. His systematic investigations of the vibrational spectroscopy of a wide class of thermotropic liquid crystals were collected in the monograph Vibrational spectroscopy of liquid crystals (1984), in which the molecular structure and properties of various liquid crystals, vibrational assignments, orientational order parameters and their calculation by molecular dynamics are presented. A range of liquid crystal materials was categorised and reported in his second book Atlas of vibrational spectra of liquid crystals (1988). Both publications remain a valuable source of information for specialists in the field of molecular spectroscopy. The outstanding contributions and growing reputation of Prof. Kirov led to periods as Visiting Scientist in the Universities of Parma, Calabria and Wroclaw. His abilities as a scientific organizer and leader were also notable, and led to a long and distinguished period of service in the Institute of Solid State Physics, being first appointed in 1980 as Scientific Secretary, and subsequently as Head of the Laboratory of Optics and Spectroscopy (1990-1998) and Director of the Institute (1991-1999). He was Chairman of the Scientific Council of ISSP over this period, and a member of the Specialized Scientific Council on Condensed Matter Physics. Prof. Kirov was a member of the High Testimonial Committee of the Republic of Bulgaria during 1996. Nikolay Kirov was a key figure in the organization, promotion and success of the International School on Condensed Matter Physics (ISCMP), where he was able to use his network of international contacts to excellent effect. He served as Scientific Secretary (1988-1990), Chairman and Editor of the ISCMP Proceedings (1992-1998), and as Chairman Emeritus (2002-2012). Prof. Kirov is an Honorary Member of the Institute of Solid State Physics. He received the Honorary Diploma 'Nicola Obreshkov' in 1986 and the "Marin Drinov" Sign of Honour BAS (on a ribbon) in 1998, for achievements in the physical and mathematical sciences. He was also honoured outside his native Bulgaria, receiving a Gold Medal from Wroclaw University, Poland, in recognition of successful scientific collaborations in the area of molecular structure.

How Molecular Structure Affects Mechanical Properties of an Advanced Polymer

NASA Technical Reports Server (NTRS)

Nicholson, Lee M.; Whitley, Karen S.; Gates, Thomas S.; Hinkley, Jeffrey A.

2000-01-01

density was performed over a range of temperatures below the glass transition temperature. The physical characterization, elastic properties and notched tensile strength all as a function of molecular weight and test temperature were determined. For the uncrosslinked SI material, it was shown that notched tensile strength is a strong function of both temperature and molecular weight, whereas stiffness is only a strong function of temperature. For the crosslinked PETI-SI material, it was shown that the effect of crosslinking significantly enhances the mechanical performance of the low molecular weight material; comparable to that exhibited by the high molecular weight material.

[Molecular imaging; current status and future prospects in USA].

PubMed

Kobayashi, Hisataka

2007-02-01

The goal of this review is to introduce the definition, current status, and future prospects of the molecular imaging, which has recently been a hot topic in medicine and the biological science in USA. In vivo imaging methods to visualize the molecular events and functions in organs or animals/humans are overviewed and discussed especially in combinations of imaging modalities (machines) and contrast agents(chemicals) used in the molecular imaging. Next, the close relationship between the molecular imaging and the nanotechnology, an important part of nanomedicine, is stressed from the aspect of united multidisciplinary sciences such as physics, chemistry, biology, and medicine.

The Computer Simulation of Liquids by Molecular Dynamics.

ERIC Educational Resources Information Center

Smith, W.

1987-01-01

Proposes a mathematical computer model for the behavior of liquids using the classical dynamic principles of Sir Isaac Newton and the molecular dynamics method invented by other scientists. Concludes that other applications will be successful using supercomputers to go beyond simple Newtonian physics. (CW)

Fullerenes, carbon nanotubes, and graphene for molecular electronics.

PubMed

Pinzón, Julio R; Villalta-Cerdas, Adrián; Echegoyen, Luis

2012-01-01

With the constant growing complexity of electronic devices, the top-down approach used with silicon based technology is facing both technological and physical challenges. Carbon based nanomaterials are good candidates to be used in the construction of electronic circuitry using a bottom-up approach, because they have semiconductor properties and dimensions within the required physical limit to establish electrical connections. The unique electronic properties of fullerenes for example, have allowed the construction of molecular rectifiers and transistors that can operate with more than two logical states. Carbon nanotubes have shown their potential to be used in the construction of molecular wires and FET transistors that can operate in the THz frequency range. On the other hand, graphene is not only the most promising material for replacing ITO in the construction of transparent electrodes but it has also shown quantum Hall effect and conductance properties that depend on the edges or chemical doping. The purpose of this review is to present recent developments on the utilization carbon nanomaterials in molecular electronics.

Magnetismo Molecular (Molecular Magentism)

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

Reis, Mario S; Moreira Dos Santos, Antonio F

The new synthesis processes in chemistry open a new world of research, new and surprising materials never before found in nature can now be synthesized and, as a wonderful result, observed a series of physical phenomena never before imagined. Among these are many new materials the molecular magnets, the subject of this book and magnetic properties that are often reflections of the quantum behavior of these materials. Aside from the wonderful experience of exploring something new, the theoretical models that describe the behavior these magnetic materials are, in most cases, soluble analytically, which allows us to know in detail themore » physical mechanisms governing these materials. Still, the academic interest in parallel this subject, these materials have a number of properties that are promising to be used in technological devices, such as in computers quantum magnetic recording, magnetocaloric effect, spintronics and many other devices. This volume will journey through the world of molecular magnets, from the structural description of these materials to state of the art research.« less

PREFACE: Sixth International Conference on Dissociative Recombination: Theory, Experiments and Applications

NASA Astrophysics Data System (ADS)

Wolf, Andreas; Lammich, Lutz; Schmelcher, Peter

2005-01-01

Dissociative recombination between electrons and molecular ions is an elementary reaction in electron-induced chemistry attracting strong attention across discipline boundaries, from fundamental questions of intramolecular dynamics to astrophysics, plasma science, as well as atmospheric and planetary physics. The process is explored on the level of atomic quantum dynamics both experimentally and theoretically, employing cold collisions at temperatures down to 10 Kelvin involving small molecules or also very large systems ranging up to biomolecules. Dissociative recombination (DR) and related processes, such as dissociative excitation, collisional cooling of vibrations and rotations, photodissociation via high-lying electronic states, resonant electron attachment, and electron-induced processes in large molecules and clusters, are studied by a variety of experimental methods, including stored and trapped molecular ions, plasma techniques such as stationary and flowing afterglow, and laser spectroscopic diagnostic of molecular excitations. The Sixth International Conference on Dissociative Recombination: Theory, Experiments and Applications (DR2004) was organized by the Research Group on Atomic and Molecular Physics with Stored Ions at the Max-Planck Institute for Nuclear Physics in Heidelberg, Germany, and held near Heidelberg in the town of Mosbach in July 2004. It was attended by about 90 scientists working in atomic and molecular physics, astrophysics, plasma- and biophysics. International Conferences on Dissociative Recombination and related processes were held before at Lake Louise, Alberta, Canada (1988), Saint Jacut, Brittany, France (1992), Ein Gedi, Israel (1995), Nässlingen, Stockholm Archipelago, Sweden (1999), and last within a symposium at the American Chemical Society meeting in Chicago, USA (2001). The presentations of this conference document a strong development of theoretical ideas towards the understanding of DR in particular in polyatomic systems. Strong attention was given to the elementary triatomic benchmark system H3+, characterized by ambitious, complementary experimental projects. Interaction of experiment and theory improves in particular the understanding of non-adiabatic molecular interactions involving electronic continuum states. New experimental techniques focus on a detailed control of the internal molecular excitation on the level of single quantum states, which gives increasing importance to laser interactions and ion storage at cryogenic temperatures. Apart from its place in the series of "DR conferences", this meeting is also the final assembly of the EU Research Training Network "Electron Transfer Reactions" (ETR) which in the period from 2000 to 2004 helped to establish many invaluable links between 15 experimental and theoretical institutes active in the field of DR and related processes. We express our gratitude to the EU for the support through the Research Training Network Programme, which has made possible the attendance of many students and young researchers. Furthermore, generous financial support for this conference was provided by the Max-Planck Institute for Nuclear Physics in Heidelberg. The efficient support of the conference center "Alte Mälzerei", operated by the city of Mosbach, is gratefully acknowledged. Finally we warmly thank the staff and the students of the Max-Planck Institute for Nuclear Physics for the dedicated help during the conference.

[Cii] emission from L1630 in the Orion B molecular cloud.

PubMed

Pabst, C H M; Goicoechea, J R; Teyssier, D; Berné, O; Ochsendorf, B B; Wolfire, M G; Higgins, R D; Riquelme, D; Risacher, C; Pety, J; Le Petit, F; Roueff, E; Bron, E; Tielens, A G G M

2017-10-01

L1630 in the Orion B molecular cloud, which includes the iconic Horsehead Nebula, illuminated by the star system σ Ori, is an example of a photodissociation region (PDR). In PDRs, stellar radiation impinges on the surface of dense material, often a molecular cloud, thereby inducing a complex network of chemical reactions and physical processes. Observations toward L1630 allow us to study the interplay between stellar radiation and a molecular cloud under relatively benign conditions, that is, intermediate densities and an intermediate UV radiation field. Contrary to the well-studied Orion Molecular Cloud 1 (OMC1), which hosts much harsher conditions, L1630 has little star formation. Our goal is to relate the [Cii] fine-structure line emission to the physical conditions predominant in L1630 and compare it to studies of OMC1. The [Cii] 158 μ m line emission of L1630 around the Horsehead Nebula, an area of 12' × 17', was observed using the upgraded German Receiver for Astronomy at Terahertz Frequencies (upGREAT) onboard the Stratospheric Observatory for Infrared Astronomy (SOFIA). Of the [Cii] emission from the mapped area 95%, 13 L ⊙ , originates from the molecular cloud; the adjacent Hii region contributes only 5%, that is, 1 L ⊙ . From comparison with other data (CO(1-0)-line emission, far-infrared (FIR) continuum studies, emission from polycyclic aromatic hydrocarbons (PAHs)), we infer a gas density of the molecular cloud of n H ∼ 3 · 10 3 cm -3 , with surface layers, including the Horsehead Nebula, having a density of up to n H ∼ 4 · 10 4 cm -3 . The temperature of the surface gas is T ∼ 100 K. The average [Cii] cooling efficiency within the molecular cloud is 1.3 · 10 -2 . The fraction of the mass of the molecular cloud within the studied area that is traced by [Cii] is only 8%. Our PDR models are able to reproduce the FIR-[Cii] correlations and also the CO(1-0)-[Cii] correlations. Finally, we compare our results on the heating efficiency of the gas with theoretical studies of photoelectric heating by PAHs, clusters of PAHs, and very small grains, and find the heating efficiency to be lower than theoretically predicted, a continuation of the trend set by other observations. In L1630 only a small fraction of the gas mass is traced by [Cii]. Most of the [Cii] emission in the mapped area stems from PDR surfaces. The layered edge-on structure of the molecular cloud and limitations in spatial resolution put constraints on our ability to relate different tracers to each other and to the physical conditions. From our study, we conclude that the relation between [Cii] emission and physical conditions is likely to be more complicated than often assumed. The theoretical heating efficiency is higher than the one we calculate from the observed [Cii] emission in the L1630 molecular cloud.

[Cii] emission from L1630 in the Orion B molecular cloud

PubMed Central

Pabst, C. H. M.; Goicoechea, J. R.; Teyssier, D.; Berné, O.; Ochsendorf, B. B.; Wolfire, M. G.; Higgins, R. D.; Riquelme, D.; Risacher, C.; Pety, J.; Le Petit, F.; Roueff, E.; Bron, E.; Tielens, A. G. G. M.

2017-01-01

Context L1630 in the Orion B molecular cloud, which includes the iconic Horsehead Nebula, illuminated by the star system σ Ori, is an example of a photodissociation region (PDR). In PDRs, stellar radiation impinges on the surface of dense material, often a molecular cloud, thereby inducing a complex network of chemical reactions and physical processes. Aims Observations toward L1630 allow us to study the interplay between stellar radiation and a molecular cloud under relatively benign conditions, that is, intermediate densities and an intermediate UV radiation field. Contrary to the well-studied Orion Molecular Cloud 1 (OMC1), which hosts much harsher conditions, L1630 has little star formation. Our goal is to relate the [Cii] fine-structure line emission to the physical conditions predominant in L1630 and compare it to studies of OMC1. Methods The [Cii] 158 μm line emission of L1630 around the Horsehead Nebula, an area of 12′ × 17′, was observed using the upgraded German Receiver for Astronomy at Terahertz Frequencies (upGREAT) onboard the Stratospheric Observatory for Infrared Astronomy (SOFIA). Results Of the [Cii] emission from the mapped area 95%, 13 L⊙, originates from the molecular cloud; the adjacent Hii region contributes only 5%, that is, 1 L⊙. From comparison with other data (CO(1-0)-line emission, far-infrared (FIR) continuum studies, emission from polycyclic aromatic hydrocarbons (PAHs)), we infer a gas density of the molecular cloud of nH ∼ 3 · 103 cm−3, with surface layers, including the Horsehead Nebula, having a density of up to nH ∼ 4 · 104 cm−3. The temperature of the surface gas is T ∼ 100 K. The average [Cii] cooling efficiency within the molecular cloud is 1.3 · 10−2. The fraction of the mass of the molecular cloud within the studied area that is traced by [Cii] is only 8%. Our PDR models are able to reproduce the FIR-[Cii] correlations and also the CO(1-0)-[Cii] correlations. Finally, we compare our results on the heating efficiency of the gas with theoretical studies of photoelectric heating by PAHs, clusters of PAHs, and very small grains, and find the heating efficiency to be lower than theoretically predicted, a continuation of the trend set by other observations. Conclusions In L1630 only a small fraction of the gas mass is traced by [Cii]. Most of the [Cii] emission in the mapped area stems from PDR surfaces. The layered edge-on structure of the molecular cloud and limitations in spatial resolution put constraints on our ability to relate different tracers to each other and to the physical conditions. From our study, we conclude that the relation between [Cii] emission and physical conditions is likely to be more complicated than often assumed. The theoretical heating efficiency is higher than the one we calculate from the observed [Cii] emission in the L1630 molecular cloud. PMID:28989177

Modeling of metal thin film growth: Linking angstrom-scale molecular dynamics results to micron-scale film topographies

NASA Astrophysics Data System (ADS)

Hansen, U.; Rodgers, S.; Jensen, K. F.

2000-07-01

A general method for modeling ionized physical vapor deposition is presented. As an example, the method is applied to growth of an aluminum film in the presence of an ionized argon flux. Molecular dynamics techniques are used to examine the surface adsorption, reflection, and sputter reactions taking place during ionized physical vapor deposition. We predict their relative probabilities and discuss their dependence on energy and incident angle. Subsequently, we combine the information obtained from molecular dynamics with a line of sight transport model in a two-dimensional feature, incorporating all effects of reemission and resputtering. This provides a complete growth rate model that allows inclusion of energy- and angular-dependent reaction rates. Finally, a level-set approach is used to describe the morphology of the growing film. We thus arrive at a computationally highly efficient and accurate scheme to model the growth of thin films. We demonstrate the capabilities of the model predicting the major differences on Al film topographies between conventional and ionized sputter deposition techniques studying thin film growth under ionized physical vapor deposition conditions with different Ar fluxes.

Molecular Factors Governing the Liquid and Glassy States Recrystallization of Celecoxib in Binary Mixtures with Excipients of Different Molecular Weights.

PubMed

Grzybowska, K; Chmiel, K; Knapik-Kowalczuk, J; Grzybowski, A; Jurkiewicz, K; Paluch, M

2017-04-03

Transformation of poorly water-soluble crystalline pharmaceuticals to the amorphous form is one of the most promising strategies to improve their oral bioavailability. Unfortunately, the amorphous drugs are usually thermodynamically unstable and may quickly return to their crystalline form. A very promising way to enhance the physical stability of amorphous drugs is to prepare amorphous compositions of APIs with certain excipients which can be characterized by significantly different molecular weights, such as polymers, acetate saccharides, and other APIs. By using different experimental techniques (broadband dielectric spectroscopy, differential scanning calorimetry, X-ray diffraction) we compare the effect of adding the large molecular weight polymer-polyvinylpyrrolidone (PVP K30)-and the small molecular weight excipient-octaacetylmaltose (acMAL)-on molecular dynamics as well as the tendency to recrystallization of the amorphous celecoxib (CEL) in the amorphous solid dispersions: CEL-PVP and CEL-acMAL. The physical stability investigations of the binary systems were performed in both the supercooled liquid and glassy states. We found that acMAL is a better inhibitor of recrystallization of amorphous CEL than PVP K30 deep in the glassy state (T < T g ). In contrast, PVP K30 is a better crystallization inhibitor of CEL than acMAL in the supercooled liquid state (at T > T g ). We discuss molecular factors governing the recrystallization of amorphous CEL in examined solid dispersions.

Recovering the Physical Properties of Molecular Gas in Galaxies from CO SLED Modeling

NASA Astrophysics Data System (ADS)

Kamenetzky, J.; Privon, G. C.; Narayanan, D.

2018-05-01

Modeling of the spectral line energy distribution (SLED) of the CO molecule can reveal the physical conditions (temperature and density) of molecular gas in Galactic clouds and other galaxies. Recently, the Herschel Space Observatory and ALMA have offered, for the first time, a comprehensive view of the rotational J = 4‑3 through J = 13‑12 lines, which arise from a complex, diverse range of physical conditions that must be simplified to one, two, or three components when modeled. Here we investigate the recoverability of physical conditions from SLEDs produced by galaxy evolution simulations containing a large dynamical range in physical properties. These simulated SLEDs were generally fit well by one component of gas whose properties largely resemble or slightly underestimate the luminosity-weighted properties of the simulations when clumping due to nonthermal velocity dispersion is taken into account. If only modeling the first three rotational lines, the median values of the marginalized parameter distributions better represent the luminosity-weighted properties of the simulations, but the uncertainties in the fitted parameters are nearly an order of magnitude, compared to approximately 0.2 dex in the “best-case” scenario of a fully sampled SLED through J = 10‑9. This study demonstrates that while common CO SLED modeling techniques cannot reveal the underlying complexities of the molecular gas, they can distinguish bulk luminosity-weighted properties that vary with star formation surface densities and galaxy evolution, if a sufficient number of lines are detected and modeled.

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.

Soft matter food physics—the physics of food and cooking

NASA Astrophysics Data System (ADS)

Vilgis, Thomas A.

2015-12-01

This review discusses the (soft matter) physics of food. Although food is generally not considered as a typical model system for fundamental (soft matter) physics, a number of basic principles can be found in the interplay between the basic components of foods, water, oil/fat, proteins and carbohydrates. The review starts with the introduction and behavior of food-relevant molecules and discusses food-relevant properties and applications from their fundamental (multiscale) behavior. Typical food aspects from ‘hard matter systems’, such as chocolates or crystalline fats, to ‘soft matter’ in emulsions, dough, pasta and meat are covered and can be explained on a molecular basis. An important conclusion is the point that the macroscopic properties and the perception are defined by the molecular interplay on all length and time scales.

M4Ag44(p-MBA)30 Molecular Nanoparticles

NASA Astrophysics Data System (ADS)

Conn, Brian E.

In recent years, molecular nanoparticles have attracted much attention due to their unique physical, optical, and electronic properties. The properties of molecular nanoparticles are shown to deviate from their larger bulk counterparts, due to quantum confinement effects and large surface-to-volume ratios. As the size of the nanoparticle shrinks to a cluster of metal atoms (<3 nm in diameter), there is an emergence of a HOMO-LUMO band gap, which is not present in transitional d-block metals. The HOMO-LUMO band gap gives rise to discrete electronic states, leading to new chemical and physical properties. Molecular nanoparticles have had a substantial impact across a diverse range of fields, including catalysis, sensing, photochemistry, optoelectronic, energy conversion, and medicine. Currently many of the synthetic procedures for molecular nanoparticles require low temperatures, long incubation times, multistep purification and hazardous reagents that produce low yields and polydisperse molecular nanoparticles with poor stability. Although silver has very desirable physical properties, good relative abundance and low cost, gold molecular nanoparticles have been widely favored owing to their proved stability and ease of use. Unlike gold, silver is notorious for its susceptibility to oxidation, i.e., tarnishing, which has limited the development of silver-based nanotechnologies. Despite two decades of synthetic efforts, silver molecular nanoparticles that are inert or have long-term stability have remained unrealized. Herein we report a simple synthetic protocol for producing ultrastable M4Ag44(p-MBA)30 nanoparticles as a single-sized molecular product and in exceptionally large quantities. The stability, purity, and yield are substantially better than other metal nanoparticles, including gold, due to several stabilization mechanisms. Also, reported are the structural and mechanical properties of extended crystalline solids of Na4Ag44(p-MBA)30 from large-scale quantum-mechanical simulations based on the atomically-precise X-ray measured structure. Calculations show that cohesion is derived from hydrogen bonds between bundled p-MBA ligands and that the superlattice's mechanical response to hydrostatic compression is characterized by a molecular-solid-like bulk modulus B0 = 16.7 GPa, exhibiting anomalous pressure softening and a compression-induced transition to a soft-solid phase. Such a transition involves ligand flexure, which causes gear-like correlated chiral rotation of the nanoparticles.

Boundary conditions for the paleoenvironment: Chemical and physical processes in the pre-solar nebula. [molecular clouds, interstellar matter, and abundance

NASA Technical Reports Server (NTRS)

Irvine, W. M.; Schloerb, F. P.

1985-01-01

Two additional hyperfine components of the interstellar radical C3H were detected. In addition, methanol was discovered in interstellar clouds. The abundance of HCCN and various chemical isomers in molecular clouds was investigated.

The Physical Reality of Molecules: They're Dense and They Move Around!

ERIC Educational Resources Information Center

Silverstein, Todd P.

1995-01-01

Describes a simple and graphic demonstration of molecular motion that utilizes a hot plate, a beaker, tap water, India ink, and a Pasteur pipette with a rubber bulb. Provides tips on guiding students to an understanding of molecular motion using this demonstration. (DDR)

Direction of Translation and Size of Bacteriophage φX174 Cistrons

PubMed Central

Benbow, Robert M.; Mayol, Robert F.; Picchi, Joanna C.; Sinsheimer, Robert L.

1972-01-01

Translation of the bacteriophage φX174 genome follows cistron order D-E-F-G-H-A-B-C. To establish this, the position of a nonsense mutation on the genetic map was compared with the physical size (molecular weight) of the appropriate protein fragment generated in nonpermissive cells. Distances on the φX174 genetic map and distances on a physical map constructed from the molecular weights of φX174 proteins and protein fragments are proportional over most of the genome with the exception of the high recombination region within cistron A. Images PMID:16789133

Physical and molecular bases of protein thermal stability and cold adaptation.

PubMed

Pucci, Fabrizio; Rooman, Marianne

2017-02-01

The molecular bases of thermal and cold stability and adaptation, which allow proteins to remain folded and functional in the temperature ranges in which their host organisms live and grow, are still only partially elucidated. Indeed, both experimental and computational studies fail to yield a fully precise and global physical picture, essentially because all effects are context-dependent and thus quite intricate to unravel. We present a snapshot of the current state of knowledge of this highly complex and challenging issue, whose resolution would enable large-scale rational protein design. Copyright © 2016 Elsevier Ltd. All rights reserved.

Advances in modelling of biomimetic fluid flow at different scales

PubMed Central

2011-01-01

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

Molecular Knots

PubMed Central

Fielden, Stephen D. P.; Woltering, Steffen L.

2017-01-01

Abstract The first synthetic molecular trefoil knot was prepared in the late 1980s. However, it is only in the last few years that more complex small‐molecule knot topologies have been realized through chemical synthesis. The steric restrictions imposed on molecular strands by knotting can impart significant physical and chemical properties, including chirality, strong and selective ion binding, and catalytic activity. As the number and complexity of accessible molecular knot topologies increases, it will become increasingly useful for chemists to adopt the knot terminology employed by other disciplines. Here we give an overview of synthetic strategies towards molecular knots and outline the principles of knot, braid, and tangle theory appropriate to chemistry and molecular structure. PMID:28477423

MRI of chemical reactions and processes.

PubMed

Britton, Melanie M

2017-08-01

As magnetic resonance imaging (MRI) can spatially resolve a wealth of molecular information available from nuclear magnetic resonance (NMR), it is able to non-invasively visualise the composition, properties and reactions of a broad range of spatially-heterogeneous molecular systems. Hence, MRI is increasingly finding applications in the study of chemical reactions and processes in a diverse range of environments and technologies. This article will explain the basic principles of MRI and how it can be used to visualise chemical composition and molecular properties, providing an overview of the variety of information available. Examples are drawn from the disciplines of chemistry, chemical engineering, environmental science, physics, electrochemistry and materials science. The review introduces a range of techniques used to produce image contrast, along with the chemical and molecular insight accessible through them. Methods for mapping the distribution of chemical species, using chemical shift imaging or spatially-resolved spectroscopy, are reviewed, as well as methods for visualising physical state, temperature, current density, flow velocities and molecular diffusion. Strategies for imaging materials with low signal intensity, such as those containing gases or low sensitivity nuclei, using compressed sensing, para-hydrogen or polarisation transfer, are discussed. Systems are presented which encapsulate the diversity of chemical and physical parameters observable by MRI, including one- and two-phase flow in porous media, chemical pattern formation, phase transformations and hydrodynamic (fingering) instabilities. Lastly, the emerging area of electrochemical MRI is discussed, with studies presented on the visualisation of electrochemical deposition and dissolution processes during corrosion and the operation of batteries, supercapacitors and fuel cells. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

USSR and Eastern Europe Scientific Abstracts Physics and Mathematics No. 35

DTIC Science & Technology

1977-06-15

depends on the film thickness, on the conditions of demagnetization , and on the constant of uniaxial magnetic anisotropy. The distribution of...Acoustics 2 Crystals and Semiconductors.. .*. 16 Electricity and Magnetism 51 Fluid Dynamics 64 Lasers and Masers 88 Magnetohydrodynamics 110...Molecular Physics 132 Nuclear Physics 133 Optics and Spectroscopy 158 Stress, Strain and Deformation 165 Superconductivity 170 Theoretical

Teaching symmetry in the introductory physics curriculum

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

Hill, C. T.; Lederman, L. M.

Modern physics is largely defined by fundamental symmetry principles and Noether's Theorem. Yet these are not taught, or rarely mentioned, to beginning students, thus missing an opportunity to reveal that the subject of physics is as lively and contemporary as molecular biology, and as beautiful as the arts. We prescribe a symmetry module to insert into the curriculum, of a week's length.

Interface between Physics and Biology: Training a New Generation of Creative Bilingual Scientists.

PubMed

Riveline, Daniel; Kruse, Karsten

2017-08-01

Whereas physics seeks for universal laws underlying natural phenomena, biology accounts for complexity and specificity of molecular details. Contemporary biological physics requires people capable of working at this interface. New programs prepare scientists who transform respective disciplinary views into innovative approaches for solving outstanding problems in the life sciences. Copyright © 2017 Elsevier Ltd. All rights reserved.

Modifying Effects of Plasticizer, Chain Connectivity, and Chain Adsorption on the Physical Aging and Interfacial Gradient in Dynamics in Thin Polystyrene Films

NASA Astrophysics Data System (ADS)

Thees, Michael; Roth, Connie

How the glass transition and physical aging in thin films change with confinement is nontrival, with studies in the literature showing that these effects can be modified by various factors including chain adsorption to substrate interfaces and addition of diluents. Some studies indicate that addition of plasticizer appears to eliminate confinement effects such as Tg gradients and possibly impacts chain adsorption to substrates. In contrast, how plasticizer affects physical aging in glassy polymers has been largely unexplored experimentally, despite various theoretical and simulation efforts. Previously we have shown that for neat polystyrene (PS) films, with molecular weights MW < 3000 kg/mol, physical aging rates in thin films decrease with decreasing film thickness consistent with expectations from local Tg gradients. However, we have recently found that for very high molecular weights, MW > 7000 kg/mol, the physical aging rate in thin films was more bulk like, suggesting a diminished gradient in dynamics related to chain connectivity and possibly chain adsorption to the substrate interface. Here, we explore how the addition of dioctyl phthalate (DOP) plasticizer to PS can alter the physical aging rate of thin films and possibly modify the adsorbed layer.

DNA, RNA and the Physical Basis of Life

ERIC Educational Resources Information Center

Fong, Peter

1969-01-01

Presents the application of knowledge in the physical sciences to biological science problems, including those in the behavioral sciences, social sciences, and the humanities. Examples are presented in the areas of molecular psychology and theoretical biology, besides the principal genetic discussion. (RR)

Stochastic fundamental diagram for probabilistic traffic flow modeling.

DOT National Transportation Integrated Search

2011-09-01

Flowing water in river, transported gas or oil in pipe, electric current in wire, moving : goods on conveyor, molecular motors in living cell, and driving vehicles on a highway are : various kinds of flow from physical or non-physical systems, yet ea...

CALCULATING PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FOR ENVIRONMENTAL MODELING FROM MOLECULAR STRUCTURE

EPA Science Inventory

Mathematical models for predicting the transport and fate of pollutants in the environment require reactivity parameter values-- that is value of the physical and chemical constants that govern reactivity. Although empirical structure activity relationships have been developed t...

Physics and Its Interfaces with Medicinal Chemistry and Drug Design

NASA Astrophysics Data System (ADS)

Santos, Ricardo N.; Andricopulo, Adriano D.

2013-08-01

Medicinal chemistry is a multidisciplinary subject that integrates knowledge from a variety of fields of science, including, but not limited to, chemistry, biology, and physics. The area of drug design involves the cooperative work of scientists with a diverse range of backgrounds and technical skills, trying to tackle complex problems using an integration of approaches and methods. One important contribution to this field comes from physics through studies that attempt to identify and quantify the molecular interactions between small molecules (drugs) and biological targets (receptors), such as the forces that govern the interactions, the thermodynamics of the drug-receptor interactions, and so on. In this context, the interfaces of physics, medicinal chemistry, and drug design are of vital importance for the development of drugs that not only have the right chemistry but also the right intermolecular properties to interact at the macromolecular level, providing useful information about the principles and molecular mechanisms underlying the therapeutic action of drugs. This article highlights some of the most important connections between physics and medicinal chemistry in the design of new drugs.

Database-Driven Analyses of Astronomical Spectra

NASA Astrophysics Data System (ADS)

Cami, Jan

2012-03-01

Spectroscopy is one of the most powerful tools to study the physical properties and chemical composition of very diverse astrophysical environments. In principle, each nuclide has a unique set of spectral features; thus, establishing the presence of a specific material at astronomical distances requires no more than finding a laboratory spectrum of the right material that perfectly matches the astronomical observations. Once the presence of a substance is established, a careful analysis of the observational characteristics (wavelengths or frequencies, intensities, and line profiles) allows one to determine many physical parameters of the environment in which the substance resides, such as temperature, density, velocity, and so on. Because of this great diagnostic potential, ground-based and space-borne astronomical observatories often include instruments to carry out spectroscopic analyses of various celestial objects and events. Of particular interest is molecular spectroscopy at infrared wavelengths. From the spectroscopic point of view, molecules differ from atoms in their ability to vibrate and rotate, and quantum physics inevitably causes those motions to be quantized. The energies required to excite vibrations or rotations are such that vibrational transitions generally occur at infrared wavelengths, whereas pure rotational transitions typically occur at sub-mm wavelengths. Molecular vibration and rotation are coupled though, and thus at infrared wavelengths, one commonly observes a multitude of ro-vibrational transitions (see Figure 13.1). At lower spectral resolution, all transitions blend into one broad ro-vibrational molecular band. The isotope. Molecular spectroscopy thus allows us to see a difference of one neutron in an atomic nucleus that is located at astronomical distances! Since the detection of the first interstellar molecules (the CH [21] and CN [14] radicals), more than 150 species have been detected in space, ranging in size from diatomic species to the fullerene species C60 and C70 [4]. Given the large number and variety of molecules detected in space, molecular infrared spectroscopy can be used to study pretty much any astrophysical environment that is not too energetic to dissociate the molecules. At the lowest energies, it is interesting to note that molecules such as CN have been used to measure the temperature of the Cosmic Microwave Background (see e.g., Ref. 15). The great diagnostic potential of infrared molecular spectroscopy comes at a price though. Extracting the physical parameters from the observations requires expertise in knowing how various physical processes and instrumental characteristics play together in producing the observed spectra. In addition to the astronomical aspects, this often includes interpreting and understanding the limitations of laboratory data and quantum-chemical calculations; the study of the interaction of matter with radiation at microscopic scales (called radiative transfer, akin to ray tracing) and the effects of observing (e.g., smoothing and resampling) on the resulting spectra and possible instrumental effects (e.g., fringes). All this is not trivial. To make matters worse, observational spectra often contain many components, and might include spectral contributions stemming from very different physical conditions. Fully analyzing such observations is thus a time-consuming task that requires mastery of several techniques. And with ever-increasing rates of observational data acquisition, it seems clear that in the near future, some form of automation is required to handle the data stream. It is thus appealing to consider what part of such analyses could be done without too much human intervention. Two different aspects can be separated: the first step involves simply identifying the molecular species present in the observations. Once the molecular inventory is known, we can try to extract the physical parameters from the observed spectral properties. For both steps, good databases of molecular spectroscopic information is vital; the second step furthermore requires a good understanding of how these spectral properties change for each of the physical parameters of interest. Here, we will first present a general strategy using a convenient and powerful computational tool. We will then show two different, specific examples of analyses where some fundamental spectroscopic information is available in (a) database(s), and where that information has been successfully used to analyze observations. Whereas these examples do not directly address the question of automated analyses, they offer some insight into the possibilities and difficulties one can expect to encounter on this quest. In Section 13.2, we first describe the general formalism and method that we will be using, and we offer a few general considerations about what is involved in modeling. In Section 13.3, we illustrate our method for the case of polycyclic aromatic hydrocarbons (PAHs). In Section 13.4,we show how the same approach can be slightly modified to extract physical parameters from infrared observations of red giant stars. We then come back to the question of automated spectral analyses in Section 13.5. precise shape of molecular bands depends primarily on the temperature of the gas, and infrared observations of molecular bands can thus be used to probe gas at temperatures as low as 10 K and up to a few thousand K. Similarly, molecular band shapes contain some information about the gas densities. The resulting ro-vibrational spectrum is truly unique for each molecular species, just as is the case for atoms.As a telling example, Figure 13.2 illustrates how we can even discriminate between different isotopologues - two species with the same chemical formula and structure, but where one (or more) of the atoms is a different

Molecular medicine - To be or not to be.

PubMed

Brunori, Maurizio; Gianni, Stefano

2016-01-01

Molecular medicine is founded on the synergy between Chemistry, Physics, Biology and Medicine, with the ambitious goal of tackling diseases from a molecular perspective. This Review aims at retracing a personal outlook of the birth and development of molecular medicine, as well as at highlighting some of the most urgent challenges linked to aging and represented by incurable neurodegenerative diseases caused by protein misfolding. Furthermore, we emphasize the emerging role of the retromer dysfunctions and improper protein sorting in Alzheimer's disease and other important neurological disordered. Copyright © 2016 Elsevier B.V. All rights reserved.

Derivatives of Ergot-alkaloids: Molecular structure, physical properties, and structure-activity relationships

NASA Astrophysics Data System (ADS)

Ivanova, Bojidarka B.; Spiteller, Michael

2012-09-01

A comprehensive screening of fifteen functionalized Ergot-alkaloids, containing bulk aliphatic cyclic substituents at D-ring of the ergoline molecular skeleton was performed, studying their structure-active relationships and model interactions with α2A-adreno-, serotonin (5HT2A) and dopamine D3 (D3A) receptors. The accounted high affinity to the receptors binding loops and unusual bonding situations, joined with the molecular flexibility of the substituents and the presence of proton accepting/donating functional groups in the studied alkaloids, may contribute to further understanding the mechanisms of biological activity in vivo and in predicting their therapeutic potential in central nervous system (CNS), including those related the Schizophrenia. Since the presented correlation between the molecular structure and properties, was based on the comprehensively theoretical computational and experimental physical study on the successfully isolated derivatives, through using routine synthetic pathways in a relatively high yields, marked these derivatives as 'treasure' for further experimental and theoretical studied in areas such as: (a) pharmacological and clinical testing; (b) molecular-drugs design of novel psychoactive substances; (c) development of the analytical protocols for determination of Ergot-alkaloids through a functionalization of the ergoline-skeleton, and more.

An integrated molecular cytogenetic map of Cucumis sativus L. chromosome 2.

PubMed

Han, Yonghua; Zhang, Zhonghua; Huang, Sanwen; Jin, Weiwei

2011-01-27

Integration of molecular, genetic and cytological maps is still a challenge for most plant species. Recent progress in molecular and cytogenetic studies created a basis for developing integrated maps in cucumber (Cucumis sativus L.). In this study, eleven fosmid clones and three plasmids containing 45S rDNA, the centromeric satellite repeat Type III and the pericentriomeric repeat CsRP1 sequences respectively were hybridized to cucumber metaphase chromosomes to assign their cytological location on chromosome 2. Moreover, an integrated molecular cytogenetic map of cucumber chromosomes 2 was constructed by fluorescence in situ hybridization (FISH) mapping of 11 fosmid clones together with the cucumber centromere-specific Type III sequence on meiotic pachytene chromosomes. The cytogenetic map was fully integrated with genetic linkage map since each fosmid clone was anchored by a genetically mapped simple sequence repeat marker (SSR). The relationship between the genetic and physical distances along chromosome was analyzed. Recombination was not evenly distributed along the physical length of chromosome 2. Suppression of recombination was found in centromeric and pericentromeric regions. Our results also indicated that the molecular markers composing the linkage map for chromosome 2 provided excellent coverage of the chromosome.

Measurement Frontiers in Molecular Biology

NASA Astrophysics Data System (ADS)

Laderman, Stephen

2009-03-01

Developments of molecular measurements and manipulations have long enabled forefront research in evolution, genetics, biological development and its dysfunction, and the impact of external factors on the behavior of cells. Measurement remains at the heart of exciting and challenging basic and applied problems in molecular and cell biology. Methods to precisely determine the identity and abundance of particular molecules amongst a complex mixture of similar and dissimilar types require the successful design and integration of multiple steps involving biochemical manipulations, separations, physical probing, and data processing. Accordingly, today's most powerful methods for characterizing life at the molecular level depend on coordinated advances in applied physics, biochemistry, chemistry, computer science, and engineering. This is well illustrated by recent approaches to the measurement of DNA, RNA, proteins, and intact cells. Such successes underlie well founded visions of how molecular biology can further assist in answering compelling scientific questions and in enabling the development of remarkable advances in human health. These visions, in turn, are motivating the interdisciplinary creation of even more comprehensive measurements. As a further and closely related consequence, they are motivating innovations in the conceptual and practical approaches to organizing and visualizing large, complex sets of interrelated experimental results and distilling from those data compelling, informative conclusions.

Molecular aspects of aromatic C additions to soils: Implications of char quality for ecosystem functionality

NASA Astrophysics Data System (ADS)

Keiluweit, M.; Nico, P. S.; Johnson, M. G.; Kleber, M.

2009-12-01

Solid residues of incomplete combustion (biochar or char) are continuously being added to soils due to natural vegetation fires in many ecosystems. However, new strategies for carbon sequestration in soils are likely to include the active addition of biochar to soils. Since biochar is a highly aromatic organic material such additions will modify the native molecular structure of soil organic matter and thus alter interactions with the global atmosphere and hydrosphere. Here we present a molecular level assessment of the physical organization and chemical complexity of biomass-derived chars and, specifically, that of aromatic carbon in char structures. Differences among wood and grass charred at temperatures from 100 to 700°C are investigated. BET-N2 surface area, X-ray diffraction (XRD), synchrotron-based Near-edge X-ray Absorption Fine Structure (NEXAFS) and Fourier transform infrared (FT-IR) spectroscopy results demonstrate how the two plant precursor materials undergo analogous, but quantitatively different physical-chemical transitions as charring intensity increases. These changes suggest the existence of four distinct physical and chemical categories of char. We find that each category of char consists of a unique mixture of chemical phases and physical states: (i) in transition chars the crystalline character of the precursor materials is preserved, (ii) in amorphous chars the heat-altered molecules and incipient aromatic polycondensates are randomly mixed, (iii) composite chars consist of poorly ordered graphene stacks embedded in amorphous phases, and (iv) turbostratic chars are dominated by turbostratic (disordered) graphitic crystallites. There is wide variation in both the chemical and the physical nature of aromatic carbon among these char categories. In this presentation we will point out how molecular variations among the aromatic components of the different char categories translate into differences in their ability to: (i) persist in the environment, (ii) function as environmental sorbents, and (iii) to enable the soil to provide environmental services.

Evolution viewed from physics, physiology and medicine.

PubMed

Noble, Denis

2017-10-06

Stochasticity is harnessed by organisms to generate functionality. Randomness does not, therefore, necessarily imply lack of function or 'blind chance' at higher levels. In this respect, biology must resemble physics in generating order from disorder. This fact is contrary to Schrödinger's idea of biology generating phenotypic order from molecular- level order, which inspired the central dogma of molecular biology. The order originates at higher levels, which constrain the components at lower levels. We now know that this includes the genome, which is controlled by patterns of transcription factors and various epigenetic and reorganization mechanisms. These processes can occur in response to environmental stress, so that the genome becomes 'a highly sensitive organ of the cell' (McClintock). Organisms have evolved to be able to cope with many variations at the molecular level. Organisms also make use of physical processes in evolution and development when it is possible to arrive at functional development without the necessity to store all information in DNA sequences. This view of development and evolution differs radically from that of neo-Darwinism with its emphasis on blind chance as the origin of variation. Blind chance is necessary, but the origin of functional variation is not at the molecular level. These observations derive from and reinforce the principle of biological relativity, which holds that there is no privileged level of causation. They also have important implications for medical science.

Modelling dishes and exploring culinary 'precisions': the two issues of molecular gastronomy.

PubMed

This, Hervé

2005-04-01

The scientific strategy of molecular gastronomy includes modelling 'culinary definitions' and experimental explorations of 'culinary precisions'. A formalism that describes complex dispersed systems leads to a physical classification of classical sauces, as well as to the invention of an infinite number of new dishes.

The Physics of Coupled Atomic-Molecular Condensate System

DTIC Science & Technology

2010-10-09

electric dipoles represents a novel state of matter with long-range and anisotropic dipole-dipole interactions, that are highly amenable to the...free-bound FC factor. Simultaneously, a series of laser �elds of (molecular) Rabi frequency i (i 2) are applied to move the molecules from the

Crystallographic Determination of Molecular Parameters for K2SiF6: A Physical Chemistry Laboratory Experiment.

ERIC Educational Resources Information Center

Loehlin, James H.; Norton, Alexandra P.

1988-01-01

Describes a crystallography experiment using both diffraction-angle and diffraction-intensity information to determine the lattice constant and a lattice independent molecular parameter, while still employing standard X-ray powder diffraction techniques. Details the method, experimental details, and analysis for this activity. (CW)

Molecular alterations in skeletal muscle in rheumatoid arthritis are related to disease activity, physical inactivity, and disability.

PubMed

Huffman, Kim M; Jessee, Ryan; Andonian, Brian; Davis, Brittany N; Narowski, Rachel; Huebner, Janet L; Kraus, Virginia B; McCracken, Julie; Gilmore, Brian F; Tune, K Noelle; Campbell, Milton; Koves, Timothy R; Muoio, Deborah M; Hubal, Monica J; Kraus, William E

2017-01-23

To identify molecular alterations in skeletal muscle in rheumatoid arthritis (RA) that may contribute to ongoing disability in RA. Persons with seropositive or erosive RA (n = 51) and control subjects matched for age, gender, race, body mass index (BMI), and physical activity (n = 51) underwent assessment of disease activity, disability, pain, physical activity and thigh muscle biopsies. Muscle tissue was used for measurement of pro-inflammatory markers, transcriptomics, and comprehensive profiling of metabolic intermediates. Groups were compared using mixed models. Bivariate associations were assessed with Spearman correlation. Compared to controls, patients with RA had 75% greater muscle concentrations of IL-6 protein (p = 0.006). In patients with RA, muscle concentrations of inflammatory markers were positively associated (p < 0.05 for all) with disease activity (IL-1β, IL-8), disability (IL-1β, IL-6), pain (IL-1β, TNF-α, toll-like receptor (TLR)-4), and physical inactivity (IL-1β, IL-6). Muscle cytokines were not related to corresponding systemic cytokines. Prominent among the gene sets differentially expressed in muscles in RA versus controls were those involved in skeletal muscle repair processes and glycolytic metabolism. Metabolic profiling revealed 46% higher concentrations of pyruvate in muscle in RA (p < 0.05), and strong positive correlation between levels of amino acids involved in fibrosis (arginine, ornithine, proline, and glycine) and disability (p < 0.05). RA is accompanied by broad-ranging molecular alterations in skeletal muscle. Analysis of inflammatory markers, gene expression, and metabolic intermediates linked disease-related disruptions in muscle inflammatory signaling, remodeling, and metabolic programming to physical inactivity and disability. Thus, skeletal muscle dysfunction might contribute to a viscous cycle of RA disease activity, physical inactivity, and disability.

Education in applied and instrumental optics at the University of Helsinki

NASA Astrophysics Data System (ADS)

Stenman, Folke

1997-12-01

The teaching of applied and instrumental optics at the University of Helsinki Department of Physics originally grew out of the needs of the research group of molecular physics as a basis for the experimental work in the group. The training program starts with a one-year course for senior undergraduates and graduates comprising geometrical optics, eikonal theory, image forming components, matrix methods, optical instruments, the optics of laser beams, radiometry and photometry, ray tracing methods, optics of anisotropic media, diffraction theory, general image formation theory and Fourier optics. The course starts from fundamentals, but the mathematical level is kept adequate for serious work. Further applications are treated in courses on molecular spectroscopy, where ruled and holographic diffraction gratings (both plane and spherical), interferometric spectroscopy and imaging properties of spectral equipment are treated. Aspects of image analysis, information in optics, signal-to-noise ratio, etc. are treated in separate courses on Fourier method and digital spectral analysis. The applicability of optical techniques to various fields of physics and engineering and the analogies with them are especially brought out. Experimental and calculational and skills are stressed throughout. Computer programming is introduced as an indispensable tool for the optics practitioner, and the students are required to write programs of their own. The students gain practical experience, e.g., by working in the molecular physics group. Close cooperation is maintained with other research groups in laser physics, ultrasonics and physical chemistry. The training in optics has proved very useful, with students frequently ending up working in the industry on optics and spectroscopy problems. Parts of these courses have also been given at other universities and to engineers and scientists working in the industry.

Biology-inspired AMO physics

NASA Astrophysics Data System (ADS)

Mathur, Deepak

2015-01-01

This Topical Review presents an overview of increasingly robust interconnects that are being established between atomic, molecular and optical (AMO) physics and the life sciences. AMO physics, outgrowing its historical role as a facilitator—a provider of optical methodologies, for instance—now seeks to partner biology in its quest to link systems-level descriptions of biological entities to insights based on molecular processes. Of course, perspectives differ when AMO physicists and biologists consider various processes. For instance, while AMO physicists link molecular properties and dynamics to potential energy surfaces, these have to give way to energy landscapes in considerations of protein dynamics. But there are similarities also: tunnelling and non-adiabatic transitions occur both in protein dynamics and in molecular dynamics. We bring to the fore some such differences and similarities; we consider imaging techniques based on AMO concepts, like 4D fluorescence microscopy which allows access to the dynamics of cellular processes, multiphoton microscopy which offers a built-in confocality, and microscopy with femtosecond laser beams to saturate the suppression of fluorescence in spatially controlled fashion so as to circumvent the diffraction limit. Beyond imaging, AMO physics contributes with optical traps that probe the mechanical and dynamical properties of single ‘live’ cells, highlighting differences between healthy and diseased cells. Trap methodologies have also begun to probe the dynamics governing of neural stem cells adhering to each other to form neurospheres and, with squeezed light to probe sub-diffusive motion of yeast cells. Strong field science contributes not only by providing a source of energetic electrons and γ-rays via laser-plasma accelerations schemes, but also via filamentation and supercontinuum generation, enabling mainstream collision physics into play in diverse processes like DNA damage induced by low-energy collisions to invoking dissociative attachment in quantification of stress levels in humans. The prognosis is extremely good for more intense interaction of AMO physics and biology; by way of future predictions attention is drawn to only two of very many opportunities for such interactions: application of attosecond techniques and tunnelling experiments to biological problems.

Continuous All-Optical Deceleration and Single-Photon Cooling of Molecular Beams

DTIC Science & Technology

2014-02-21

PHYSICAL REVIEW A 89 , 023425 (2014) Continuous all-optical deceleration and single-photon cooling of molecular beams A. M. Jayich,1 A. C. Vutha,2 M...details including multilevel numerical simulations of strontium monohydride. These techniques are applicable to a large number of molecular species and...molecules that are considered difficult to directly laser cool—a class that includes many 1050-2947/2014/ 89 (2)/023425(8) 023425-1 ©2014 American

Atomic and molecular supernovae

NASA Technical Reports Server (NTRS)

Liu, Weihong

1997-01-01

Atomic and molecular physics of supernovae is discussed with an emphasis on the importance of detailed treatments of the critical atomic and molecular processes with the best available atomic and molecular data. The observations of molecules in SN 1987A are interpreted through a combination of spectral and chemical modelings, leading to strong constraints on the mixing and nucleosynthesis of the supernova. The non-equilibrium chemistry is used to argue that carbon dust can form in the oxygen-rich clumps where the efficient molecular cooling makes the nucleation of dust grains possible. For Type Ia supernovae, the analyses of their nebular spectra lead to strong constraints on the supernova explosion models.

Sanibel Symposium in the Petascale-Exascale Computational Era

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

Cheng, Hai-Ping

The 56 th Sanibel Symposium was held February 14-19 2016 at the King and Prince Hotel, St. Simons Island, GA. It successfully brought quantum chemists and chemical and condensed matter physicists together in presentations, posters, and informal discussions bridging those two communities. The Symposium has had a significant role in preparing generations of quantum theorists. As computational potency and algorithmic sophistication have grown, the Symposium has evolved to emphasize more heavily computationally oriented method development in chemistry and materials physics, including nanoscience, complex molecular phenomena, and even bio-molecular methods and problems. Given this context, the 56 th Sanibel meeting systematicallymore » and deliberately had sessions focused on exascale computation. A selection of outstanding theoretical problems that need serious attention was included. Five invited sessions, two contributed sessions (hot topics), and a poster session were organized with the exascale theme. This was a historic milestone in the evolution of the Symposia. Just as years ago linear algebra, perturbation theory, density matrices, and band-structure methods dominated early Sanibel Symposia, the exascale sessions of the 56 thmeeting contributed a transformative influence to add structure and strength to the computational physical science community in an unprecedented way. A copy of the full program of the 56 th Symposium is attached. The exascale sessions were Linear Scaling, Non-Adabatic Dynamics, Interpretive Theory and Models, Computation, Software, and Algorithms, and Quantum Monte Carlo. The Symposium Proceedings will be published in Molecular Physics (2017). Note that the Sanibel proceedings from 2015 and 2014 were published as Molecular Physics vol. 114, issue 3-4 (2016) and vol. 113, issue 3-4 (2015) respectively.« less

Characterization and Higher-Order Structure Assessment of an Interchain Cysteine-Based ADC: Impact of Drug Loading and Distribution on the Mechanism of Aggregation.

PubMed

Guo, Jianxin; Kumar, Sandeep; Chipley, Mark; Marcq, Olivier; Gupta, Devansh; Jin, Zhaowei; Tomar, Dheeraj S; Swabowski, Cecily; Smith, Jacquelynn; Starkey, Jason A; Singh, Satish K

2016-03-16

The impact of drug loading and distribution on higher order structure and physical stability of an interchain cysteine-based antibody drug conjugate (ADC) has been studied. An IgG1 mAb was conjugated with a cytotoxic auristatin payload following the reduction of interchain disulfides. The 2-D LC-MS analysis shows that there is a preference for certain isomers within the various drug to antibody ratios (DARs). The physical stability of the unconjugated monoclonal antibody, the ADC, and isolated conjugated species with specific DAR, were compared using calorimetric, thermal, chemical denaturation and molecular modeling techniques, as well as techniques to assess hydrophobicity. The DAR was determined to have a significant impact on the biophysical properties and stability of the ADC. The CH2 domain was significantly perturbed in the DAR6 species, which was attributable to quaternary structural changes as assessed by molecular modeling. At accelerated storage temperatures, the DAR6 rapidly forms higher molecular mass species, whereas the DAR2 and the unconjugated mAb were largely stable. Chemical denaturation study indicates that DAR6 may form multimers while DAR2 and DAR4 primarily exist in monomeric forms in solution at ambient conditions. The physical state differences were correlated with a dramatic increase in the hydrophobicity and a reduction in the surface tension of the DAR6 compared to lower DAR species. Molecular modeling of the various DAR species and their conformers demonstrates that the auristatin-based linker payload directly contributes to the hydrophobicity of the ADC molecule. Higher order structural characterization provides insight into the impact of conjugation on the conformational and colloidal factors that determine the physical stability of cysteine-based ADCs, with implications for process and formulation development.

Molecular Innovations Toward Theranostics of Aggressive Prostate Cancer

DTIC Science & Technology

2017-11-01

Department of Physics and Astronomy , Texas Christian University, Fort Worth, T xas 76129, United States, ‡Department of Chemistry and Biochemistry, Texas...E. Simanek,*,‡ and Zygmunt Gryczynski*,† †Department of Physics and Astronomy , Texas Christian University, Fort Worth, Texas 76129, United States

Polymer Principles in the Undergraduate Physical Chemistry Course. Part 2.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1985

1985-01-01

Part l (SE 538 305) covered application of classical thermodynamics, polymer crystallinity, and phase diagrams to teaching physical chemistry. This part covers statistical thermodynamics, conformation, molecular weights, rubber elasticity and viscoelasticity, and kinetics of polymerization. Eight polymer-oriented, multiple-choice test questions…

The contribution of physics to Nuclear Medicine: physicians' perspective on future directions.

PubMed

Mankoff, David A; Pryma, Daniel A

2014-12-01

Advances in Nuclear Medicine physics enabled the specialty of Nuclear Medicine and directed research in other aspects of radiotracer imaging, ultimately leading to Nuclear Medicine's emergence as an important component of current medical practice. Nuclear Medicine's unique ability to characterize in vivo biology without perturbing it will assure its ongoing role in a practice of medicine increasingly driven by molecular biology. However, in the future, it is likely that advances in molecular biology and radiopharmaceutical chemistry will increasingly direct future developments in Nuclear Medicine physics, rather than relying on physics as the primary driver of advances in Nuclear Medicine. Working hand-in-hand with clinicians, chemists, and biologists, Nuclear Medicine physicists can greatly enhance the specialty by creating more sensitive and robust imaging devices, by enabling more facile and sophisticated image analysis to yield quantitative measures of regional in vivo biology, and by combining the strengths of radiotracer imaging with other imaging modalities in hybrid devices, with the overall goal to enhance Nuclear Medicine's ability to characterize regional in vivo biology.

Influence of Molecular Weight on the Mechanical Performance of a Thermoplastic Glassy Polyimide

NASA Technical Reports Server (NTRS)

Nicholson, Lee M.; Whitley, Karen S.; Gates, Thomas S.; Hinkley, Jeffrey A.

1999-01-01

Mechanical Testing of an advanced thermoplastic polyimide (LaRC-TM-SI) with known variations in molecular weight was performed over a range of temperatures below the glass transition temperature. The physical characterization, elastic properties and notched tensile strength were all determined as a function of molecular weight and test temperature. It was shown that notched tensile strength is a strong function of both temperature and molecular weight, whereas stiffness is only a strong function of temperature. A critical molecular weight (Mc) was observed to occur at a weight-average molecular weight (Mw) of approx. 22000 g/mol below which, the notched tensile strength decreases rapidly. This critical molecular weight transition is temperature-independent. Furthermore, inelastic analysis showed that low molecular weight materials tended to fail in a brittle manner, whereas high molecular weight materials exhibited ductile failure. The microstructural images supported these findings.

Mechanisms of plastic deformation in highly cross-linked UHMWPE for total hip components--the molecular physics viewpoint.

PubMed

Takahashi, Yasuhito; Shishido, Takaaki; Yamamoto, Kengo; Masaoka, Toshinori; Kubo, Kosuke; Tateiwa, Toshiyuki; Pezzotti, Giuseppe

2015-02-01

Plastic deformation is an unavoidable event in biomedical polymeric implants for load-bearing application during long-term in-vivo service life, which involves a mass transfer process, irreversible chain motion, and molecular reorganization. Deformation-induced microstructural alterations greatly affect mechanical properties and durability of implant devices. The present research focused on evaluating, from a molecular physics viewpoint, the impact of externally applied strain (or stress) in ultra-high molecular weight polyethylene (UHMWPE) prostheses, subjected to radiation cross-linking and subsequent remelting for application in total hip arthroplasty (THA). Two different types of commercial acetabular liners, which belong to the first-generation highly cross-linked UHMWPE (HXLPE), were investigated by means of confocal/polarized Raman microprobe spectroscopy. The amount of crystalline region and the spatial distribution of molecular chain orientation were quantitatively analyzed according to a combined theory including Raman selection rules for the polyethylene orthorhombic structure and the orientation distribution function (ODF) statistical approach. The structurally important finding was that pronounced recrystallization and molecular reorientation increasingly appeared in the near-surface regions of HXLPE liners with increasing the amount of plastic (compressive) deformation stored in the microstructure. Such molecular rearrangements, occurred in response to external strains, locally increase surface cross-shear (CS) stresses, which in turn trigger microscopic wear processes in HXLPE acetabular liners. Thus, on the basis of the results obtained at the molecular scale, we emphasize here the importance of minimizing the development of irrecoverable deformation strain in order to retain the pristine and intrinsically high wear performance of HXLPE components. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular design, synthesis and physical properties of novel Cytisine-derivatives - Experimental and theoretical study

NASA Astrophysics Data System (ADS)

Ivanova, Bojidarka; Spiteller, Michael

2013-02-01

The paper presented a comprehensive theoretical and experimental study on the molecular drugs-design, synthesis, isolation, physical spectroscopic and mass spectrometric elucidation of novel functionalization derivatives of Cytisine (Cyt), using nucleosidic residues. Since these alkaloids have established biochemical profile, related the binding affinity of the nicotinic acetylcholine receptors (nAChRs), particularly α7 sub-type, the presented correlation between the molecular structure and properties allowed to evaluated the highlights of the biochemical hypothesises related the Schizophrenia. The anticancer activity of α7 subtype agonists and the crucial role of the nucleoside-based medications in the cancer therapy provided opportunity for further study on the biochemical relationship between Schizophrenia and few kinds of cancers, which has been hypothesized recently. The physical electronic absorptions (EAs), circular dichroic (CD) and Raman spectroscopic (RS) properties as well as mass spectrometric (MS) data, obtained using electrospray ionization (ESI) and atmospheric-pressure chemical ionization (APCI) methods under the positive single (MS) and tandem (MS/MS) modes of operation are discussed. Taking into account reports on a fatal intoxication of Cyt, the presented data would be of interest in the field of forensic chemistry, through development of highly selective and sensitive analytical protocols. Quantum chemical method is used to predict the physical properties of the isolated alkaloids, their affinity to the receptor loop and gas-phase stabilized species, observed mass spectrometrically.

The relationship between grain hardness, dough mixing parameters and bread-making quality in winter wheat.

PubMed

Salmanowicz, Bolesław P; Adamski, Tadeusz; Surma, Maria; Kaczmarek, Zygmunt; Karolina, Krystkowiak; Kuczyńska, Anetta; Banaszak, Zofia; Lugowska, Bogusława; Majcher, Małgorzata; Obuchowski, Wiktor

2012-01-01

The influence of grain hardness, determined by using molecular markers and physical methods (near-infrared (NIR) technique and particle size index-PSI) on dough characteristics, which in turn were determined with the use of a farinograph and reomixer, as well as bread-making properties were studied. The material covered 24 winter wheat genotypes differing in grain hardness. The field experiment was conducted at standard and increased levels of nitrogen fertilization. Results of molecular analyses were in agreement with those obtained by the use of physical methods for soft-grained lines. Some lines classified as hard (by physical methods) appeared to have the wild-type Pina and Pinb alleles, similar to soft lines. Differences in dough and bread-making properties between lines classified as hard and soft on the basis of molecular data appeared to be of less significance than the differences between lines classified as hard and soft on the basis of physical analyses of grain texture. Values of relative grain hardness at the increased nitrogen fertilization level were significantly higher. At both fertilization levels the NIR parameter determining grain hardness was significantly positively correlated with the wet gluten and sedimentation values, with most of the rheological parameters and bread yield. Values of this parameter correlated with quality characteristics in a higher degree than values of particle size index.

The Relationship Between Grain Hardness, Dough Mixing Parameters and Bread-Making Quality in Winter Wheat

PubMed Central

Salmanowicz, Bolesław P.; Adamski, Tadeusz; Surma, Maria; Kaczmarek, Zygmunt; Karolina, Krystkowiak; Kuczyńska, Anetta; Banaszak, Zofia; Ługowska, Bogusława; Majcher, Małgorzata; Obuchowski, Wiktor

2012-01-01

The influence of grain hardness, determined by using molecular markers and physical methods (near-infrared (NIR) technique and particle size index—PSI) on dough characteristics, which in turn were determined with the use of a farinograph and reomixer, as well as bread-making properties were studied. The material covered 24 winter wheat genotypes differing in grain hardness. The field experiment was conducted at standard and increased levels of nitrogen fertilization. Results of molecular analyses were in agreement with those obtained by the use of physical methods for soft-grained lines. Some lines classified as hard (by physical methods) appeared to have the wild-type Pina and Pinb alleles, similar to soft lines. Differences in dough and bread-making properties between lines classified as hard and soft on the basis of molecular data appeared to be of less significance than the differences between lines classified as hard and soft on the basis of physical analyses of grain texture. Values of relative grain hardness at the increased nitrogen fertilization level were significantly higher. At both fertilization levels the NIR parameter determining grain hardness was significantly positively correlated with the wet gluten and sedimentation values, with most of the rheological parameters and bread yield. Values of this parameter correlated with quality characteristics in a higher degree than values of particle size index. PMID:22605973

Space physics educational outreach

NASA Technical Reports Server (NTRS)

Copeland, Richard A.

1995-01-01

The goal of this Space Physics Educational Outreach project was to develop a laboratory experiment and classroom lecture on Earth's aurora for use in lower division college physics courses, with the particular aim of implementing the experiment and lecture at Saint Mary's College of California. The strategy is to teach physics in the context of an interesting natural phenomenon by investigating the physical principles that are important in Earth's aurora, including motion of charged particles in electric and magnetic fields, particle collisions and chemical reactions, and atomic and molecular spectroscopy. As a by-product, the undergraduate students would develop an appreciation for naturally occurring space physics phenomena.

Photoassisted physical vapor epitaxial growth of semiconductors: a review of light-induced modifications to growth processes

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

Alberi, Kirstin; Scarpulla, Michael A.

Herein, we review the remarkable range of modifications to materials properties associated with photoexcitation of the growth surface during physical vapor epitaxy of semiconductors. We concentrate on mechanisms producing measureable, utilizable changes in crystalline perfection, phase, composition, doping, and defect distribution. We outline the relevant physics of different mechanisms, concentrating on those yielding effects orthogonal to the primary growth variables of temperature and atomic or molecular fluxes and document the phenomenological effects reported. Based on experimental observations from a range of semiconductor systems and growth conditions, the primary effects include enhanced anion desorption, molecular dissociation, increased doping efficiency, modification tomore » defect populations and improvements to the crystalline quality of epilayers grown at low temperatures. Future research directions and technological applications are also discussed.« less

Chance, necessity and the origins of life: a physical sciences perspective

NASA Astrophysics Data System (ADS)

Hazen, Robert M.

2017-11-01

Earth's 4.5-billion-year history has witnessed a complex sequence of high-probability chemical and physical processes, as well as `frozen accidents'. Most models of life's origins similarly invoke a sequence of chemical reactions and molecular self-assemblies in which both necessity and chance play important roles. Recent research adds two important insights into this discussion. First, in the context of chemical reactions, chance versus necessity is an inherently false dichotomy-a range of probabilities exists for many natural events. Second, given the combinatorial richness of early Earth's chemical and physical environments, events in molecular evolution that are unlikely at limited laboratory scales of space and time may, nevertheless, be inevitable on an Earth-like planet at time scales of a billion years. This article is part of the themed issue 'Reconceptualizing the origins of life'.

The impact of recent advances in laboratory astrophysics on our understanding of the cosmos.

PubMed

Savin, D W; Brickhouse, N S; Cowan, J J; Drake, R P; Federman, S R; Ferland, G J; Frank, A; Gudipati, M S; Haxton, W C; Herbst, E; Profumo, S; Salama, F; Ziurys, L M; Zweibel, E G

2012-03-01

An emerging theme in modern astrophysics is the connection between astronomical observations and the underlying physical phenomena that drive our cosmos. Both the mechanisms responsible for the observed astrophysical phenomena and the tools used to probe such phenomena-the radiation and particle spectra we observe-have their roots in atomic, molecular, condensed matter, plasma, nuclear and particle physics. Chemistry is implicitly included in both molecular and condensed matter physics. This connection is the theme of the present report, which provides a broad, though non-exhaustive, overview of progress in our understanding of the cosmos resulting from recent theoretical and experimental advances in what is commonly called laboratory astrophysics. This work, carried out by a diverse community of laboratory astrophysicists, is increasingly important as astrophysics transitions into an era of precise measurement and high fidelity modeling.

Photoassisted physical vapor epitaxial growth of semiconductors: a review of light-induced modifications to growth processes

DOE PAGES

Alberi, Kirstin; Scarpulla, Michael A.

2017-11-22

Herein, we review the remarkable range of modifications to materials properties associated with photoexcitation of the growth surface during physical vapor epitaxy of semiconductors. We concentrate on mechanisms producing measureable, utilizable changes in crystalline perfection, phase, composition, doping, and defect distribution. We outline the relevant physics of different mechanisms, concentrating on those yielding effects orthogonal to the primary growth variables of temperature and atomic or molecular fluxes and document the phenomenological effects reported. Based on experimental observations from a range of semiconductor systems and growth conditions, the primary effects include enhanced anion desorption, molecular dissociation, increased doping efficiency, modification tomore » defect populations and improvements to the crystalline quality of epilayers grown at low temperatures. Future research directions and technological applications are also discussed.« less

Spatial variation of the physical conditions of molecular gas in galaxies

NASA Technical Reports Server (NTRS)

Jackson, James M.; Eckart, Andreas; Wild, Wolfgang; Genzel, Reinhard; Harris, Andrew I.; Downes, Dennis; Jaffe, D. T.; Ho, Paul T. P.

1990-01-01

Multi-line studies of CO-12, CO-13, C-18O, HCN, and HCO(+) at 3 mm, 1.3 mm, and 0.8 mm using the Institute for Radio Astronomy in the Millimeter range (IRAM) 30 m telescope, with the IRAM superconductor insulator superconductor (SIS) receivers and the Max Planck Institute for External Physics (MPE) 350 GHz SIS receiver, show that the densities and temperatures of molecular gas in external galaxies change significantly with position. CO-12 measures the densities and temperature of diffuse interclump molecular gas, but not the bulk of the molecular gas. Simple one-component models, with or without external heating, cannot account for the weakness of the CO-12 J = 3 to 2 line relative to J = 2 to 1 and J = 1 to 0. CO-12 does not trace the bulk of the molecular gas, and optical depth effects obviate a straightforward interpretation of CO-12 data. Instead, researchers turned to the optically thin CO isotopes and other molecular species. Isotopic CO lines measure the bulk of the molecular gas, and HCN and HCO(+) pick out denser regions. Researchers find a warm ridge of gas in IC 342 (Eckart et al. 1989), denser gas in the starburst nucleus of IC 342, and a possible hot-spot in NGC 2903. In IC 342, NGC 2146, and NGC 6764, the CO-13 J = 2 to 1 line is subthermally populated, implying gas densities less than or equal to 10(exp 4) cm(-3).

The Logical and Psychological Structure of Physical Chemistry and Its Relevance to the Organization/Sequencing of the Major Areas Covered in Physical Chemistry Textbooks

ERIC Educational Resources Information Center

Tsaparlis, Georgios

2014-01-01

Jensen's scheme for the logical structure of chemistry is taken as reference to study the logical structure of physical chemistry. The scheme distinguishes three dimensions (composition and structure, energy, and time), with each dimension treated at one of the three levels (molar, molecular, and electrical). Such a structure places the outer…

NUCLEAR CHEMISTRY ANNUAL REPORT 1970

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

Authors, Various

Papers are presented for the following topics: (1) Nuclear Structure and Nuclear Properties - (a) Nuclear Spectroscopy and Radioactivity; (b) Nuclear Reactions and Scattering; (c) Nuclear Theory; and (d) Fission. (2) Chemical and Atomic Physics - (a) Atomic and Molecular Spectroscopy; and (b) Hyperfine Interactions. (3) Physical, Inorganic, and Analytical Chemistry - (a) X-Ray Crystallography; (b) Physical and Inorganic Chemistry; (c) Radiation Chemistry; and (d) Chemical Engineering. (4) Instrumentation and Systems Development.

[C II] emission from L1630 in the Orion B molecular cloud

NASA Astrophysics Data System (ADS)

Pabst, C. H. M.; Goicoechea, J. R.; Teyssier, D.; Berné, O.; Ochsendorf, B. B.; Wolfire, M. G.; Higgins, R. D.; Riquelme, D.; Risacher, C.; Pety, J.; Le Petit, F.; Roueff, E.; Bron, E.; Tielens, A. G. G. M.

2017-10-01

Context. L1630 in the Orion B molecular cloud, which includes the iconic Horsehead Nebula, illuminated by the star system σ Ori, is an example of a photodissociation region (PDR). In PDRs, stellar radiation impinges on the surface of dense material, often a molecular cloud, thereby inducing a complex network of chemical reactions and physical processes. Aims: Observations toward L1630 allow us to study the interplay between stellar radiation and a molecular cloud under relatively benign conditions, that is, intermediate densities and an intermediate UV radiation field. Contrary to the well-studied Orion Molecular Cloud 1 (OMC1), which hosts much harsher conditions, L1630 has little star formation. Our goal is to relate the [C II] fine-structure line emission to the physical conditions predominant in L1630 and compare it to studies of OMC1. Methods: The [C II] 158 μm line emission of L1630 around the Horsehead Nebula, an area of 12' × 17', was observed using the upgraded German Receiver for Astronomy at Terahertz Frequencies (upGREAT) onboard the Stratospheric Observatory for Infrared Astronomy (SOFIA). Results: Of the [C II] emission from the mapped area 95%, 13 L⊙, originates from the molecular cloud; the adjacent H II region contributes only 5%, that is, 1 L⊙. From comparison with other data (CO (1 - 0)-line emission, far-infrared (FIR) continuum studies, emission from polycyclic aromatic hydrocarbons (PAHs)), we infer a gas density of the molecular cloud of nH 3 × 103 cm-3, with surface layers, including the Horsehead Nebula, having a density of up to nH 4 × 104 cm-3. The temperature of the surface gas is T 100 K. The average [C II] cooling efficiency within the molecular cloud is 1.3 × 10-2. The fraction of the mass of the molecular cloud within the studied area that is traced by [C II] is only 8%. Our PDR models are able to reproduce the FIR-[C II] correlations and also the CO (1 - 0)-[C II] correlations. Finally, we compare our results on the heating efficiency of the gas with theoretical studies of photoelectric heating by PAHs, clusters of PAHs, and very small grains, and find the heating efficiency to be lower than theoretically predicted, a continuation of the trend set by other observations. Conclusions: In L1630 only a small fraction of the gas mass is traced by [C II]. Most of the [C II] emission in the mapped area stems from PDR surfaces. The layered edge-on structure of the molecular cloud and limitations in spatial resolution put constraints on our ability to relate different tracers to each other and to the physical conditions. From our study, we conclude that the relation between [C II] emission and physical conditions is likely to be more complicated than often assumed. The theoretical heating efficiency is higher than the one we calculate from the observed [C II] emission in the L1630 molecular cloud.

Precision Spectroscopy of Molecular Hydrogen and the Search for New Physics

NASA Astrophysics Data System (ADS)

Ubachs, Wim

2017-06-01

The hydrogen molecule is the smallest neutral chemical entity and a benchmark system of molecular spectroscopy. The comparison between highly accurate measurements of transition frequencies and level energies with quantum calculations including all known phenomena (relativistic, vacuum polarization and self energy) provides a tool to search for physical phenomena in the realm of the unknown: are there forces beyond the three included in the Standard Model of physics plus gravity [1], are there extra dimensions beyond the 3+1 describing space time [2] ? Comparison of laboratory wavelengths of transitions in hydrogen may be compared with the lines observed during the epoch of the early Universe to verify whether fundamental constants of Nature have varied over cosmological time [3]. These concepts, as well as the precision laboratory experiments and the astronomical observations used for such searches of new physics [4] will be discussed. [1] E.J. Salumbides, J.C.J. Koelemeij, J. Komasa, K. Pachucki, K.S.E. Eikema, W. Ubachs, Bounds on fifth forces from precision measurements on molecules, Phys. Rev. D87, 112008 (2013). [2] E.J. Salumbides, A.N. Schellekens, B. Gato-Rivera, W. Ubachs Constraints on extra dimensions from molecular spectroscopy, New. J. Phys. 17, 033015 (2015). [3] W. Ubachs, J. Bagdonaite, E.J. Salumbides, M.T. Murphy, L. Kaper, Search for a drifting proton-electron mass ratio from H_2, Rev. Mod. Phys. 88, 021003 (2016). [4] W. Ubachs, J.C.J. Koelemeij, K.S.E. Eikema, E.J. Salumbides, Physics beyond the Standard Model from hydrogen spectroscopy, J. Mol. Spectr. 320, 1 (2016).

Integrating Computational Chemistry into the Physical Chemistry Curriculum

ERIC Educational Resources Information Center

Johnson, Lewis E.; Engel, Thomas

2011-01-01

Relatively few undergraduate physical chemistry programs integrate molecular modeling into their quantum mechanics curriculum owing to concerns about limited access to computational facilities, the cost of software, and concerns about increasing the course material. However, modeling exercises can be integrated into an undergraduate course at a…

Rotational Mobility in a Crystal Studied by Dielectric Relaxation Spectroscopy

ERIC Educational Resources Information Center

Dionisio, Madalena S. C.; Diogo, Herminio P.; Farinha, J. P. S.; Ramos, Joaquim J. Moura

2005-01-01

A laboratory experiment for undergraduate physical chemistry courses that uses the experimental technique of dielectric relaxation spectroscopy to study molecular mobility in a crystal is proposed. An experiment provides an excellent opportunity for dealing with a wide diversity of important basic concepts in physical chemistry.

PREDICTION OF THE VAPOR PRESSURE, BOILING POINT, HEAT OF VAPORIZATION AND DIFFUSION COEFFICIENT OF ORGANIC COMPOUNDS

EPA Science Inventory

The prototype computer program SPARC has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC solute-solute physical process models have been developed and tested...

Research relative to atmosphere physics and spacecraft applications studies

NASA Technical Reports Server (NTRS)

Greenwood, Stuart W.

1987-01-01

Progress is reported in several areas of research. Brief descriptions are given in each of the following areas: Spacelab data analysis; San Marco activity; Molecular physics; Stellar energy analysis; Troposphere data analysis; Voyager encounter analysis; Laser activity; Gravity wave study; Venus studies; and Shuttle environmental studies.

Molecular Model of a Quantum Dot Beyond the Constant Interaction Approximation

NASA Astrophysics Data System (ADS)

Temirov, Ruslan; Green, Matthew F. B.; Friedrich, Niklas; Leinen, Philipp; Esat, Taner; Chmielniak, Pawel; Sarwar, Sidra; Rawson, Jeff; Kögerler, Paul; Wagner, Christian; Rohlfing, Michael; Tautz, F. Stefan

2018-05-01

We present a physically intuitive model of molecular quantum dots beyond the constant interaction approximation. It accurately describes their charging behavior and allows the extraction of important molecular properties that are otherwise experimentally inaccessible. The model is applied to data recorded with a noncontact atomic force microscope on three different molecules that act as a quantum dot when attached to the microscope tip. The results are in excellent agreement with first-principles simulations.

Unifying the rotational and permutation symmetry of nuclear spin states: Schur-Weyl duality in molecular physics.

PubMed

Schmiedt, Hanno; Jensen, Per; Schlemmer, Stephan

2016-08-21

In modern physics and chemistry concerned with many-body systems, one of the mainstays is identical-particle-permutation symmetry. In particular, both the intra-molecular dynamics of a single molecule and the inter-molecular dynamics associated, for example, with reactive molecular collisions are strongly affected by selection rules originating in nuclear-permutation symmetry operations being applied to the total internal wavefunctions, including nuclear spin, of the molecules involved. We propose here a general tool to determine coherently the permutation symmetry and the rotational symmetry (associated with the group of arbitrary rotations of the entire molecule in space) of molecular wavefunctions, in particular the nuclear-spin functions. Thus far, these two symmetries were believed to be mutually independent and it has even been argued that under certain circumstances, it is impossible to establish a one-to-one correspondence between them. However, using the Schur-Weyl duality theorem we show that the two types of symmetry are inherently coupled. In addition, we use the ingenious representation-theory technique of Young tableaus to represent the molecular nuclear-spin degrees of freedom in terms of well-defined mathematical objects. This simplifies the symmetry classification of the nuclear wavefunction even for large molecules. Also, the application to reactive collisions is very straightforward and provides a much simplified approach to obtaining selection rules.

Unifying the rotational and permutation symmetry of nuclear spin states: Schur-Weyl duality in molecular physics

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

Schmiedt, Hanno; Schlemmer, Stephan; Jensen, Per, E-mail: jensen@uni-wuppertal.de

In modern physics and chemistry concerned with many-body systems, one of the mainstays is identical-particle-permutation symmetry. In particular, both the intra-molecular dynamics of a single molecule and the inter-molecular dynamics associated, for example, with reactive molecular collisions are strongly affected by selection rules originating in nuclear-permutation symmetry operations being applied to the total internal wavefunctions, including nuclear spin, of the molecules involved. We propose here a general tool to determine coherently the permutation symmetry and the rotational symmetry (associated with the group of arbitrary rotations of the entire molecule in space) of molecular wavefunctions, in particular the nuclear-spin functions. Thusmore » far, these two symmetries were believed to be mutually independent and it has even been argued that under certain circumstances, it is impossible to establish a one-to-one correspondence between them. However, using the Schur-Weyl duality theorem we show that the two types of symmetry are inherently coupled. In addition, we use the ingenious representation-theory technique of Young tableaus to represent the molecular nuclear-spin degrees of freedom in terms of well-defined mathematical objects. This simplifies the symmetry classification of the nuclear wavefunction even for large molecules. Also, the application to reactive collisions is very straightforward and provides a much simplified approach to obtaining selection rules.« less

Macroscopic contraction of a gel induced by the integrated motion of light-driven molecular motors

NASA Astrophysics Data System (ADS)

Li, Quan; Fuks, Gad; Moulin, Emilie; Maaloum, Mounir; Rawiso, Michel; Kulic, Igor; Foy, Justin T.; Giuseppone, Nicolas

2015-02-01

Making molecular machines that can be useful in the macroscopic world is a challenging long-term goal of nanoscience. Inspired by the protein machinery found in biological systems, and based on the theoretical understanding of the physics of motion at the nanoscale, organic chemists have developed a number of molecules that can produce work by contraction or rotation when triggered by various external chemical or physical stimuli. In particular, basic molecular switches that commute between at least two thermodynamic minima and more advanced molecular motors that behave as dissipative units working far from equilibrium when fuelled with external energy have been reported. However, despite recent progress, the ultimate challenge of coordinating individual molecular motors in a continuous mechanical process that can have a measurable effect at the macroscale has remained elusive. Here, we show that by integrating light-driven unidirectional molecular rotors as reticulating units in a polymer gel, it is possible to amplify their individual motions to achieve macroscopic contraction of the material. Our system uses the incoming light to operate under far-from-equilibrium conditions, and the work produced by the motor in the photostationary state is used to twist the entangled polymer chains up to the collapse of the gel. Our design could be a starting point to integrate nanomotors in metastable materials to store energy and eventually to convert it.

Rovibrational optical pumping of a molecular beam

NASA Astrophysics Data System (ADS)

Cournol, A.; Pillet, P.; Lignier, H.; Comparat, D.

2018-03-01

The preparation of molecules in well-defined internal states is essential for various studies in fundamental physics and physical chemistry. It is thus of particular interest to find methods that increase the brightness of molecular beams. Here, we report on rotational and vibrational pumpings of a supersonic beam of barium monofluoride molecules. With respect to previous works, the time scale of optical vibrational pumping has been greatly reduced by enhancing the spectral power density in the vicinity of the appropriate molecular transitions. We demonstrate a complete transfer of the rovibrational populations lying in v″=1 -3 into the vibrational ground-state v″=0 . Rotational pumping, which requires efficient vibrational pumping, has been also demonstrated. According to a Maxwell-Boltzmann description, the rotational temperature of our sample has been reduced by a factor of ˜8 . In this fashion, the population of the lowest rotational levels increased by more than one order of magnitude.

Molecular imaging and the unification of multilevel mechanisms and data in medical physics.

PubMed

Nikiforidis, George C; Sakellaropoulos, George C; Kagadis, George C

2008-08-01

Molecular imaging (MI) constitutes a recently developed approach of imaging, where modalities and agents have been reinvented and used in novel combinations in order to expose and measure biologic processes occurring at molecular and cellular levels. It is an approach that bridges the gap between modalities acquiring data from high (e.g., computed tomography, magnetic resonance imaging, and positron-emitting isotopes) and low (e.g., PCR, microarrays) levels of a biological organization. While data integration methodologies will lead to improved diagnostic and prognostic performance, interdisciplinary collaboration, triggered by MI, will result in a better perception of the underlying biological mechanisms. Toward the development of a unifying theory describing these mechanisms, medical physicists can formulate new hypotheses, provide the physical constraints bounding them, and consequently design appropriate experiments. Their new scientific and working environment calls for interventions in their syllabi to educate scientists with enhanced capabilities for holistic views and synthesis.

The physics and chemistry of the L134N molecular core

NASA Technical Reports Server (NTRS)

Swade, Daryl A.

1989-01-01

The dark cloud L134N is studied in detail via millimeter- and centimeter-wavelength emission-line spectra. A high-density core of molecular gas exists in L134N which has a kinetic temperature of about 12 K, a peak molecular hydrogen density of about 10 exp 4.5/cu cm, and a mass of about 23 solar. The core may be the site of future star formation. Maps of emission from (C-18)O, CS, H(C-13)O(+), SO, NH3, and C3H2 reveal morphologically different distributions resulting in part from both varying physical conditions within the cloud and optical depth effects. Significant differences also exist which are probably due to chemical abundance variations. A consistent set of LTE chemical abundances has been estimated at as many as seven positions, which can be used to constrain chemical models of dark clouds.

Structural characteristics of the molecular species of tetraacylglycerols in lesquerella (Physaria fendleri) oil elucidated by mass spectrometry

USDA-ARS?s Scientific Manuscript database

The structure and ratios of regioisomers of the molecular species of tetraacylglycerols affect their physical properties. They were elucidated by ESI mass spectrometry of the lithium adducts of tetraacylglycerols from the HPLC fractions of lesquerella oil. The contents of acyl and acylacyl chains at...

Using Computer Technology to Create a Revolutionary New Style of Biology.

ERIC Educational Resources Information Center

Monaghan, Peter

1993-01-01

A $13-million gift of William Gates III to the University of Washington has enabled establishment of the country's first department in molecular biotechnology, a combination of medicine and molecular biology to be practiced by researchers versed in a variety of fields, including computer science, computation, applied physics, and engineering. (MSE)

Use of Molecular Models for Active Learning in Biochemistry Lecture Courses

ERIC Educational Resources Information Center

Hageman, James H.

2010-01-01

The pedagogical value of having biochemistry and organic chemistry students build and manipulate physical models of chemical species is well established in the literature. Nevertheless, for the most part, the use of molecular models is generally limited to several laboratory exercises or to demonstrations in the classroom setting. A simple…

A Simple Molecular Dynamics Lab to Calculate Viscosity as a Function of Temperature

ERIC Educational Resources Information Center

Eckler, Logan H.; Nee, Matthew J.

2016-01-01

A simple molecular dynamics experiment is described to demonstrate transport properties for the undergraduate physical chemistry laboratory. The AMBER package is used to monitor self-diffusion in "n"-hexane. Scripts (available in the Supporting Information) make the process considerably easier for students, allowing them to focus on the…

Looking beyond Lewis Structures: A General Chemistry Molecular Modeling Experiment Focusing on Physical Properties and Geometry

ERIC Educational Resources Information Center

Linenberger, Kimberly J.; Cole, Renee S.; Sarkar, Somnath

2011-01-01

We present a guided-inquiry experiment using Spartan Student Version, ready to be adapted and implemented into a general chemistry laboratory course. The experiment provides students an experience with Spartan Molecular Modeling software while discovering the relationships between the structure and properties of molecules. Topics discussed within…

Manipulating 3D-Printed and Paper Models Enhances Student Understanding of Viral Replication

ERIC Educational Resources Information Center

Couper, Lisa; Johannes, Kristen; Powers, Jackie; Silberglitt, Matt; Davenport, Jodi

2016-01-01

Understanding key concepts in molecular biology requires reasoning about molecular processes that are not directly observable and, as such, presents a challenge to students and teachers. We ask whether novel interactive physical models and activities can help students understand key processes in viral replication. Our 3D tangible models are…

From gene to protein: A 3-week intensive course in molecular biology for physical scientists.

PubMed

Nadeau, Jay L

2009-07-01

This article describes a 3-week intensive molecular biology methods course based upon fluorescent proteins, which is successfully taught at the McGill University to advanced undergraduates and graduates in physics, chemical engineering, biomedical engineering, and medicine. No previous knowledge of biological terminology or methods is expected, so the material could readily be adapted to earlier undergraduates or students in other fields. The course emphasizes hands-on experience with one half-hour of lecture and 3 and a half hours of laboratory 4 days per week, for a total of 39 hours. The materials are simple and low in cost and all software used is free, making the budget accessible to small universities and community colleges that possess basic teaching wet labs. Conceptual understanding is reinforced with lab reports and an independent final paper on a subject of the student's choice. The final paper describes a possible thesis project, not necessarily the student's own, with assessment based upon grasping of key concepts and methods of molecular biology. Copyright © 2009 International Union of Biochemistry and Molecular Biology, Inc.

Temperature specification in atomistic molecular dynamics and its impact on simulation efficacy

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

Temperature is a vital thermodynamical function for physical systems. Knowledge of system temperature permits assessment of system ergodicity, entropy, system state and stability. Rapid theoretical and computational developments in the fields of condensed matter physics, chemistry, material science, molecular biology, nanotechnology and others necessitate clarity in the temperature specification. Temperature-based materials simulations, both standalone and distributed computing, are projected to grow in prominence over diverse research fields. In this article we discuss the apparent variability of temperature modeling formalisms used currently in atomistic molecular dynamics simulations, with respect to system energetics,dynamics and structural evolution. Commercial simulation programs, which by nature are heuristic, do not openly discuss this fundamental question. We address temperature specification in the context of atomistic molecular dynamics. We define a thermostat at 400K relative to a heat bath at 300K firstly using a modified ab-initio Newtonian method, and secondly using a Monte-Carlo method. The thermostatic vacancy formation and cohesion energies, equilibrium lattice constant for FCC copper is then calculated. Finally we compare and contrast the results.

TRIMS: Validating T2 Molecular Effects for Neutrino Mass Experiments

NASA Astrophysics Data System (ADS)

Lin, Ying-Ting; Trims Collaboration

2017-09-01

The Tritium Recoil-Ion Mass Spectrometer (TRIMS) experiment examines the branching ratio of the molecular tritium (T2) beta decay to the bound state (3HeT+). Measuring this branching ratio helps to validate the current molecular final-state theory applied in neutrino mass experiments such as KATRIN and Project 8. TRIMS consists of a magnet-guided time-of-flight mass spectrometer with a detector located on each end. By measuring the kinetic energy and time-of-flight difference of the ions and beta particles reaching the detectors, we will be able to distinguish molecular ions from atomic ones and hence derive the ratio in question. We will give an update on the apparatus, simulation software, and analysis tools, including efforts to improve the resolution of our detectors and to characterize the stability and uniformity of our field sources. We will also share our commissioning results and prospects for physics data. The TRIMS experiment is supported by U.S. Department of Energy Office of Science, Office of Nuclear Physics, Award Number DE-FG02-97ER41020.

The effect of conjugation to gold nanoparticles on the ability of low molecular weight chitosan to transfer DNA vaccine.

PubMed

Zhou, Xianfeng; Zhang, Xizhen; Yu, Xianghui; Zha, Xiao; Fu, Qiuan; Liu, Bin; Wang, Xueyun; Chen, Yan; Chen, Yue; Shan, Yaming; Jin, Yinghua; Wu, Yongge; Liu, Junqiu; Kong, Wei; Shen, Jiacong

2008-01-01

Nonviral gene delivery systems based on conventional high molecular weight chitosans are efficient as DNA vaccine delivery system, but have poor physical properties such as aggregated shapes, low solubility at neutral pH, high viscosity at concentrations used for in vivo delivery and a slow onset of action. Furthermore, Chitosan oligomers shorter than 14 monomers units were recently found to form only weak complexes with DNA, resulting in physically unstable polyplexes in vitro and in vivo. Here, low molecular weight chitosans with an average molecular mass of 6kDa (Chito6) have been covalently attached to gold nanoparticles (GNPs), and the potency of the resulting Chito6-GNPs conjugates as vectors for the delivery of plasmid DNA has been investigated in vitro and in vivo. After delivery by intramuscular immunization in BALB/c mice, the Chito6-GNPs conjugates induced an enhanced serum antibody response 10 times more potent than naked DNA vaccine. Additionally, in contrast to naked DNA, the Chito6-GNPs conjugates induced potent cytotoxic T lymphocyte responses at a low dose.

Testing the role of molecular physics in dissipative divertor operations through helium plasmas at DIII-D

DOE PAGES

Canik, John M.; Briesemeister, Alexis R.; McLean, Adam G.; ...

2017-05-10

Recent experiments in DIII-D helium plasmas are examined to resolve the role of atomic and molecular physics in major discrepancies between experiment and modeling of dissipative divertor operation. Helium operation removes the complicated molecular processes of deuterium plasmas that are a prime candidate for the inability of standard fluid models to reproduce dissipative divertor operation, primarily the consistent under-prediction of radiated power. Modeling of these experiments shows that the full divertor radiation can be accounted for, but only if measures are taken to ensure that the model reproduces the measured divertor density. Relying on upstream measurements instead results in amore » lower divertor density and radiation than is measured, indicating a need for improved modeling of the connection between the diverter and the upstream scrape-off layer. Furthermore, these results show that fluid models are able to quantitatively describe the divertor-region plasma, including radiative losses, and indicate that efforts to improve the fidelity of the molecular deuterium models are likely to help resolve the discrepancy in radiation for deuterium plasmas.« less

Transport in Physical Space: The Example of Pedestrians, Cars, and Molecular Motors

NASA Astrophysics Data System (ADS)

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

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

QED Tests and Search for New Physics in Molecular Hydrogen

NASA Astrophysics Data System (ADS)

Salumbides, E. J.; Niu, M. L.; Dickenson, G. D.; Eikema, K. S. E.; Komasa, J.; Pachucki, K.; Ubachs, W.

2013-06-01

The hydrogen molecule has been the benchmark system for quantum chemistry, and may provide a test ground for new physics. We present our high-resolution spectroscopic studies on the X ^1Σ^+_g electronic ground state rotational series and fundamenal vibrational tones in molecular hydrogen. In combination with recent accurate ab initio calculations, we demonstrate systematic tests of quantum electrodynamical (QED) effects in molecules. Moreover, the precise comparison between theory and experiment can provide stringent constraints on possible new interactions that extend beyond the Standard Model. E. J. Salumbides, G. D. Dickenson, T. I. Ivanov and W. Ubachs, Phys. Rev. Lett. 107, 043005 (2011).

Mechanical design of DNA nanostructures.

PubMed

Castro, Carlos E; Su, Hai-Jun; Marras, Alexander E; Zhou, Lifeng; Johnson, Joshua

2015-04-14

Structural DNA nanotechnology is a rapidly emerging field that has demonstrated great potential for applications such as single molecule sensing, drug delivery, and templating molecular components. As the applications of DNA nanotechnology expand, a consideration of their mechanical behavior is becoming essential to understand how these structures will respond to physical interactions. This review considers three major avenues of recent progress in this area: (1) measuring and designing mechanical properties of DNA nanostructures, (2) designing complex nanostructures based on imposed mechanical stresses, and (3) designing and controlling structurally dynamic nanostructures. This work has laid the foundation for mechanically active nanomachines that can generate, transmit, and respond to physical cues in molecular systems.

Measuring the Internal Structure and Physical Conditions in Star and Planet Forming Clouds Core: Toward a Quantitative Description of Cloud Evolution

NASA Technical Reports Server (NTRS)

Lada, Charles J.

2005-01-01

This grant funds a research program to use infrared extinction measurements to probe the detailed structure of dark molecular cloud cores and investigate the physical conditions which give rise to star and planet formation. The goals of this program are to acquire, reduce and analyze deep infrared and molecular-line observations of a carefully selected sample of nearby dark clouds in order to internal structure of starless cloud cores and to quantitatively investigate the evolution of such structure through the star and planet formation process. During the second year of this grant, progress toward these goals is discussed.

Application of the Finite Element Method in Atomic and Molecular Physics

NASA Technical Reports Server (NTRS)

Shertzer, Janine

2007-01-01

The finite element method (FEM) is a numerical algorithm for solving second order differential equations. It has been successfully used to solve many problems in atomic and molecular physics, including bound state and scattering calculations. To illustrate the diversity of the method, we present here details of two applications. First, we calculate the non-adiabatic dipole polarizability of Hi by directly solving the first and second order equations of perturbation theory with FEM. In the second application, we calculate the scattering amplitude for e-H scattering (without partial wave analysis) by reducing the Schrodinger equation to set of integro-differential equations, which are then solved with FEM.

Measuring the Internal Structure and Physical Conditions in Star and Planet Forming Clouds Cores: Towards a Quantitative Description of Cloud Evolution

NASA Technical Reports Server (NTRS)

Lada, Charles J.

2004-01-01

This grant funds a research program to use infrared extinction measurements to probe the detailed structure of dark molecular cloud cores and investigate the physical conditions which give rise to star and planet formation. The goals of this program are to acquire, reduce and analyze deep infrared and molecular-line observations of a carefully selected sample of nearby dark clouds in order to determine the detailed initial conditions for star formation from quantitative measurements of the internal structure of starless cloud cores and to quantitatively investigate the evolution of such structure through the star and planet formation process.

S&MPO - An information system for ozone spectroscopy on the WEB

NASA Astrophysics Data System (ADS)

Babikov, Yurii L.; Mikhailenko, Semen N.; Barbe, Alain; Tyuterev, Vladimir G.

2014-09-01

Spectroscopy and Molecular Properties of Ozone ("S&MPO") is an Internet accessible information system devoted to high resolution spectroscopy of the ozone molecule, related properties and data sources. S&MPO contains information on original spectroscopic data (line positions, line intensities, energies, transition moments, spectroscopic parameters) recovered from comprehensive analyses and modeling of experimental spectra as well as associated software for data representation written in PHP Java Script, C++ and FORTRAN. The line-by-line list of vibration-rotation transitions and other information is organized as a relational database under control of MySQL database tools. The main S&MPO goal is to provide access to all available information on vibration-rotation molecular states and transitions under extended conditions based on extrapolations of laboratory measurements using validated theoretical models. Applications for the S&MPO may include: education/training in molecular physics, radiative processes, laser physics; spectroscopic applications (analysis, Fourier transform spectroscopy, atmospheric optics, optical standards, spectroscopic atlases); applications to environment studies and atmospheric physics (remote sensing); data supply for specific databases; and to photochemistry (laser excitation, multiphoton processes). The system is accessible via Internet on two sites: http://smpo.iao.ru and http://smpo.univ-reims.fr.

Molecular Dynamics, Recrystallization Behavior, and Water Solubility of the Amorphous Anticancer Agent Bicalutamide and Its Polyvinylpyrrolidone Mixtures.

PubMed

Szczurek, Justyna; Rams-Baron, Marzena; Knapik-Kowalczuk, Justyna; Antosik, Agata; Szafraniec, Joanna; Jamróz, Witold; Dulski, Mateusz; Jachowicz, Renata; Paluch, Marian

2017-04-03

In this paper, we investigated the molecular mobility and physical stability of amorphous bicalutamide, a poorly water-soluble drug widely used in prostate cancer treatment. Our broadband dielectric spectroscopy measurements and differential scanning calorimetry studies revealed that amorphous BIC is a moderately fragile material with a strong tendency to recrystallize from the amorphous state. However, mixing the drug with polymer polyvinylpyrrolidone results in a substantial improvement of physical stability attributed to the antiplasticizing effect governed by the polymer additive. Furthermore, IR study demonstrated the existence of specific interactions between the drug and excipient. We found out that preparation of bicalutamide-polyvinylpyrrolidone mixture in a 2-1 weight ratio completely hinder material recrystallization. Moreover, we determined the time-scale of structural relaxation in the glassy state for investigated materials. Because molecular mobility is considered an important factor governing crystallization behavior, such information was used to approximate the long-term physical stability of an amorphous drug and drug-polymer systems upon their storage at room temperature. Moreover, we found that such systems have distinctly higher water solubility and dissolution rate in comparison to the pure amorphous form, indicating the genuine formulation potential of the proposed approach.

Shannon Meets Fick on the Microfluidic Channel: Diffusion Limit to Sum Broadcast Capacity for Molecular Communication.

PubMed

Bicen, A Ozan; Lehtomaki, Janne J; Akyildiz, Ian F

2018-03-01

Molecular communication (MC) over a microfluidic channel with flow is investigated based on Shannon's channel capacity theorem and Fick's laws of diffusion. Specifically, the sum capacity for MC between a single transmitter and multiple receivers (broadcast MC) is studied. The transmitter communicates by using different types of signaling molecules with each receiver over the microfluidic channel. The transmitted molecules propagate through microfluidic channel until reaching the corresponding receiver. Although the use of different types of molecules provides orthogonal signaling, the sum broadcast capacity may not scale with the number of the receivers due to physics of the propagation (interplay between convection and diffusion based on distance). In this paper, the performance of broadcast MC on a microfluidic chip is characterized by studying the physical geometry of the microfluidic channel and leveraging the information theory. The convergence of the sum capacity for microfluidic broadcast channel is analytically investigated based on the physical system parameters with respect to the increasing number of molecular receivers. The analysis presented here can be useful to predict the achievable information rate in microfluidic interconnects for the biochemical computation and microfluidic multi-sample assays.

Radiological and Environmental Research Division annual report, October 1978-September 1979. Part I. Fundamental molecular physics and chemistry

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

Not Available

1979-01-01

Research on the chemical physics of atoms and molecules, especially their interaction with external agents such as photons and electrons is reported. Abstracts of seven individual items from the report were prepared separately for the data base. (GHT)

Fundamental Studies in the Molecular Basis of Laser Induced Retinal Damage

DTIC Science & Technology

1988-01-01

Cornell University School of Applied & Engineering Physics Ithaca, NY 14853 DOD DISTRIBUTION STATEMENT Approved for public release; distribution unlimited...Code) 7b. ADDRESS (City, State, and ZIP Code) School of Applied & Engineering Physics Ithaca, NY 14853 8a. NAME OF FUNDING/SPONSORING Bb. OFFICE SYMBOL

Fundamental Studies in the Molecular Basis of Laser Induced Retinal Damage

DTIC Science & Technology

1988-01-01

Cornell University .LECT l School of Applied & Engineering PhysicsIthaca, NY 14853 0 JAN 198D DOD DISTRIBUTION STATEMENT Approved for public release...State, and ZIP Code) 7b. ADDRESS (City, State, and ZIP Code) School of Applied & Engineering Physics Ithaca, NY 14853 Ba. NAME OF FUNDING/ SPONSORING

Recent development of nanoparticles for molecular imaging

NASA Astrophysics Data System (ADS)

Kim, Jonghoon; Lee, Nohyun; Hyeon, Taeghwan

2017-10-01

Molecular imaging enables us to non-invasively visualize cellular functions and biological processes in living subjects, allowing accurate diagnosis of diseases at early stages. For successful molecular imaging, a suitable contrast agent with high sensitivity is required. To date, various nanoparticles have been developed as contrast agents for medical imaging modalities. In comparison with conventional probes, nanoparticles offer several advantages, including controllable physical properties, facile surface modification and long circulation time. In addition, they can be integrated with various combinations for multimodal imaging and therapy. In this opinion piece, we highlight recent advances and future perspectives of nanomaterials for molecular imaging. This article is part of the themed issue 'Challenges for chemistry in molecular imaging'.

Surface enhanced Raman scattering on Tardigrada--towards monitoring and imaging molecular structures in live cryptobiotic organisms.

PubMed

Kneipp, Harald; Møbjerg, Nadja; Jørgensen, Aslak; Bohr, Henrik G; Hélix-Nielsen, Claus; Kneipp, Janina; Kneipp, Katrin

2013-10-01

Tardigrades are microscopic metazoans which are able to survive extreme physical and chemical conditions by entering a stress tolerant state called cryptobiosis. At present, the molecular mechanisms behind cryptobiosis are still poorly understood. We show that surface enhanced Raman scattering supported by plasmonic gold nanoparticles can measure molecular constituents and their local distribution in live tardigrades. Surface enhanced Raman signatures allow to differentiate between two species and indicate molecular structural differences between tardigrades in water and in a dry state. This opens new avenues for exploring cryptobiosis by studying molecular changes in live cryptobiotic organisms. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamics and kinetics of reversible homo-molecular dimerization of polycyclic aromatic hydrocarbons

NASA Astrophysics Data System (ADS)

Mao, Qian; Ren, Yihua; Luo, K. H.; van Duin, Adri C. T.

2017-12-01

Physical dimerization of polycyclic aromatic hydrocarbons (PAHs) has been investigated via molecular dynamics (MD) simulation with the ReaxFF reactive force field that is developed to bridge the gap between the quantum mechanism and classical MD. Dynamics and kinetics of homo-molecular PAH collision under different temperatures, impact parameters, and orientations are studied at an atomic level, which is of great value to understand and model the PAH dimerization. In the collision process, the enhancement factors of homo-molecular dimerizations are quantified and found to be larger at lower temperatures or with smaller PAH instead of size independent. Within the capture radius, the lifetime of the formed PAH dimer decreases as the impact parameter increases. Temperature and PAH characteristic dependent forward and reverse rate constants of homo-molecular PAH dimerization are derived from MD simulations, on the basis of which a reversible model is developed. This model can predict the tendency of PAH dimerization as validated by pyrene dimerization experiments [H. Sabbah et al., J. Phys. Chem. Lett. 1(19), 2962 (2010)]. Results from this study indicate that the physical dimerization cannot be an important source under the typical flame temperatures and PAH concentrations, which implies a more significant role played by the chemical route.

Modeling Far-UV Fluorescent Emission Features of Warm Molecular Hydrogen in the Inner Regions of Protoplanetary Disks

NASA Astrophysics Data System (ADS)

Hoadley, Keri; France, Kevin

2015-01-01

Probing the surviving molecular gas within the inner regions of protoplanetary disks (PPDs) around T Tauri stars (1 - 10 Myr) provides insight into the conditions in which planet formation and migration occurs while the gas disk is still present. We model observed far ultraviolet (FUV) molecular hydrogen (H₂) fluorescent emission lines that originate within the inner regions (< 10 AU) of 9 well-studied Classic T Tauri stars, using the Hubble Space Telescope Cosmic Origins Spectrograph (COS), to explore the physical structure of the molecular disk at different PPD dust evolutionary stages. We created a 2D radiative transfer model that estimates the density and temperature distributions of warm, inner radial H₂ (T > 1500 K) with a set of 6 free parameters and produces a data cube of expected emission line profiles that describe the physical structure of the inner molecular disk atmosphere. By comparing the modeled emission lines with COS H₂ fluorescence emission features, we estimate the physical structure of the molecular disk atmosphere for each target with the set of free parameters that best replicate the observed lines. First results suggest that, for all dust evolutionary stages of disks considered, ground-state H₂ populations are described by a roughly constant temperature T(H₂) = 2500 +/- 1000 K. Possible evolution of the density structure of the H₂ atmosphere between intact and depleting dust disks may be distinguishable, but large errors in the inferred best-fit parameter sets prevent us from making this conclusion. Further improvements to the modeling framework and statistical comparison in determining the best-fit model-to-data parameter sets are ongoing, beginning with improvements to the radiative transfer model and use of up-to-date HI Lyman α absorption optical depths (see McJunkin in posters) to better estimate disk structural parameters. Once improvements are implemented, we will investigate the possible presence of a molecular wind component in the observed H₂ fluorescence features by determining blue-shifted flux residuals in the data after best-fit model-to-data comparisons are complete.

An Easily Constructed and Versatile Molecular Model

NASA Astrophysics Data System (ADS)

Hernandez, Sandra A.; Rodriguez, Nora M.; Quinzani, Oscar

1996-08-01

Three-dimensional molecular models are powerful tools used in basic courses of general and organic chemistry when the students must visualize the spatial distributions of atoms in molecules and relate them to the physical and chemical properties of such molecules. This article discusses inexpensive, easily carried, and semipermanent molecular models that the students may build by themselves. These models are based upon two different types of arrays of thin flexible wires, like telephone hook-up wires, which may be bent easily but keep their shapes.

Analysis of Physical and Numerical Factors for Prediction of UV Radiation from High Altitude Two-Phase Plumes

DTIC Science & Technology

2008-05-30

varies from continuum inside the nozzle, to transitional in the near field, to free molecular in the far field of the plume. The scales of interest vary...unity based on the rocket length. This results in the formation of a viscous shock layer characterized by a bimodal molecular velocity distribution. The...transfer model. Previous analysis21 have shown that the heat transfer model implemented in CFD++ is reproduced closely by the free molecular model

Chance, necessity and the origins of life: a physical sciences perspective.

PubMed

Hazen, Robert M

2017-12-28

Earth's 4.5-billion-year history has witnessed a complex sequence of high-probability chemical and physical processes, as well as 'frozen accidents'. Most models of life's origins similarly invoke a sequence of chemical reactions and molecular self-assemblies in which both necessity and chance play important roles. Recent research adds two important insights into this discussion. First, in the context of chemical reactions, chance versus necessity is an inherently false dichotomy-a range of probabilities exists for many natural events. Second, given the combinatorial richness of early Earth's chemical and physical environments, events in molecular evolution that are unlikely at limited laboratory scales of space and time may, nevertheless, be inevitable on an Earth-like planet at time scales of a billion years.This article is part of the themed issue 'Reconceptualizing the origins of life'. © 2017 The Author(s).

Viscosity of Common Seed and Vegetable Oils

NASA Astrophysics Data System (ADS)

Wes Fountain, C.; Jennings, Jeanne; McKie, Cheryl K.; Oakman, Patrice; Fetterolf, Monty L.

1997-02-01

Viscosity experiments using Ostwald-type gravity flow viscometers are not new to the physical chemistry laboratory. Several physical chemistry laboratory texts (1 - 3) contain at least one experiment studying polymer solutions or other well-defined systems. Several recently published articles (4 - 8) indicated the continued interest in using viscosity measurements in the teaching lab to illustrate molecular interpretation of bulk phenomena. Most of these discussions and teaching experiments are designed around an extensive theory of viscous flow and models of molecular shape that allow a full data interpretation to be attempted. This approach to viscosity experiments may not be appropriate for all teaching situations (e.g., high schools, general chemistry labs, and nonmajor physical chemistry labs). A viscosity experiment is presented here that is designed around common seed and vegetable oils. With the importance of viscosity to foodstuffs (9) and the importance of fatty acids to nutrition (10), an experiment using these common, recognizable oils has broad appeal.

Automated sampling assessment for molecular simulations using the effective sample size

PubMed Central

Zhang, Xin; Bhatt, Divesh; Zuckerman, Daniel M.

2010-01-01

To quantify the progress in the development of algorithms and forcefields used in molecular simulations, a general method for the assessment of the sampling quality is needed. Statistical mechanics principles suggest the populations of physical states characterize equilibrium sampling in a fundamental way. We therefore develop an approach for analyzing the variances in state populations, which quantifies the degree of sampling in terms of the effective sample size (ESS). The ESS estimates the number of statistically independent configurations contained in a simulated ensemble. The method is applicable to both traditional dynamics simulations as well as more modern (e.g., multi–canonical) approaches. Our procedure is tested in a variety of systems from toy models to atomistic protein simulations. We also introduce a simple automated procedure to obtain approximate physical states from dynamic trajectories: this allows sample–size estimation in systems for which physical states are not known in advance. PMID:21221418

Diffusion-controlled interface kinetics-inclusive system-theoretic propagation models for molecular communication systems

NASA Astrophysics Data System (ADS)

Chude-Okonkwo, Uche A. K.; Malekian, Reza; Maharaj, B. T.

2015-12-01

Inspired by biological systems, molecular communication has been proposed as a new communication paradigm that uses biochemical signals to transfer information from one nano device to another over a short distance. The biochemical nature of the information transfer process implies that for molecular communication purposes, the development of molecular channel models should take into consideration diffusion phenomenon as well as the physical/biochemical kinetic possibilities of the process. The physical and biochemical kinetics arise at the interfaces between the diffusion channel and the transmitter/receiver units. These interfaces are herein termed molecular antennas. In this paper, we present the deterministic propagation model of the molecular communication between an immobilized nanotransmitter and nanoreceiver, where the emission and reception kinetics are taken into consideration. Specifically, we derived closed-form system-theoretic models and expressions for configurations that represent different communication systems based on the type of molecular antennas used. The antennas considered are the nanopores at the transmitter and the surface receptor proteins/enzymes at the receiver. The developed models are simulated to show the influence of parameters such as the receiver radius, surface receptor protein/enzyme concentration, and various reaction rate constants. Results show that the effective receiver surface area and the rate constants are important to the system's output performance. Assuming high rate of catalysis, the analysis of the frequency behavior of the developed propagation channels in the form of transfer functions shows significant difference introduce by the inclusion of the molecular antennas into the diffusion-only model. It is also shown that for t > > 0 and with the information molecules' concentration greater than the Michaelis-Menten kinetic constant of the systems, the inclusion of surface receptors proteins and enzymes in the models makes the system act like a band-stop filter over an infinite frequency range.

Molecular Force Spectroscopy on Cells

NASA Astrophysics Data System (ADS)

Liu, Baoyu; Chen, Wei; Zhu, Cheng

2015-04-01

Molecular force spectroscopy has become a powerful tool to study how mechanics regulates biology, especially the mechanical regulation of molecular interactions and its impact on cellular functions. This force-driven methodology has uncovered a wealth of new information of the physical chemistry of molecular bonds for various biological systems. The new concepts, qualitative and quantitative measures describing bond behavior under force, and structural bases underlying these phenomena have substantially advanced our fundamental understanding of the inner workings of biological systems from the nanoscale (molecule) to the microscale (cell), elucidated basic molecular mechanisms of a wide range of important biological processes, and provided opportunities for engineering applications. Here, we review major force spectroscopic assays, conceptual developments of mechanically regulated kinetics of molecular interactions, and their biological relevance. We also present current challenges and highlight future directions.

Chirality in molecular collision dynamics

NASA Astrophysics Data System (ADS)

Lombardi, Andrea; Palazzetti, Federico

2018-02-01

Chirality is a phenomenon that permeates the natural world, with implications for atomic and molecular physics, for fundamental forces and for the mechanisms at the origin of the early evolution of life and biomolecular homochirality. The manifestations of chirality in chemistry and biochemistry are numerous, the striking ones being chiral recognition and asymmetric synthesis with important applications in molecular sciences and in industrial and pharmaceutical chemistry. Chiral discrimination phenomena, due to the existence of two enantiomeric forms, very well known in the case of interaction with light, but still nearly disregarded in molecular collision studies. Here we review some ideas and recent advances about the role of chirality in molecular collisions, designing and illustrating molecular beam experiments for the demonstration of chiral effects and suggesting a scenario for a stereo-directional origin of chiral selection.

Comparing Classical Water Models Using Molecular Dynamics to Find Bulk Properties

ERIC Educational Resources Information Center

Kinnaman, Laura J.; Roller, Rachel M.; Miller, Carrie S.

2018-01-01

A computational chemistry exercise for the undergraduate physical chemistry laboratory is described. In this exercise, students use the molecular dynamics package Amber to generate trajectories of bulk liquid water for 4 different water models (TIP3P, OPC, SPC/E, and TIP4Pew). Students then process the trajectory to calculate structural (radial…

Foundational Concepts and Underlying Theories for Majors in "Biochemistry and Molecular Biology"

ERIC Educational Resources Information Center

Tansey, John T.; Baird, Teaster, Jr.; Cox, Michael M.; Fox, Kristin M.; Knight, Jennifer; Sears, Duane; Bell, Ellis

2013-01-01

Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members and science educators from around the country that focused on identifying: 1) core principles of biochemistry and molecular biology, 2) essential concepts and underlying theories from physics, chemistry, and mathematics, and 3)…

Determination of Physical and Chemical Structure of New High-Temperature Polymers

DTIC Science & Technology

toward determination of the molecular weight of both perfluorosebacate and perfluoroalkyl ether-linked polymers. In addition, solubility, thermal...thermal properties, and molecular weight. Several samples of the perfluoroalkyl bibenzoxazole polymers were examined. Considerable effort was directed...stability and subambient DTA of the perfluoroalkyl ether- linked polymers (elastomers) were investigated. Samples of the aromatic heterocyclic-ladder type

A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors.

PubMed

Glowacki, David R; O'Connor, Michael; Calabró, Gaetano; Price, James; Tew, Philip; Mitchell, Thomas; Hyde, Joseph; Tew, David P; Coughtrie, David J; McIntosh-Smith, Simon

2014-01-01

With advances in computational power, the rapidly growing role of computational/simulation methodologies in the physical sciences, and the development of new human-computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data. GPU acceleration has been key to achieving our target of 60 frames per second (FPS), giving an extremely fluid interactive experience. GPU acceleration has also allowed us to scale the system for use in immersive 360° spaces with an array of up to ten depth sensors, allowing several users to simultaneously chaperone the dynamics. The flexibility of our platform for carrying out molecular dynamics simulations has been considerably enhanced by wrappers that facilitate fast communication with a portable selection of GPU-accelerated molecular force evaluation routines. In this paper, we describe a 360° atmospheric molecular dynamics simulation we have run in a chemistry/physics education context. We also describe initial tests in which users have been able to chaperone the dynamics of 10-alanine peptide embedded in an explicit water solvent. Using this system, both expert and novice users have been able to accelerate peptide rare event dynamics by 3-4 orders of magnitude.

Simulation and understanding of atomic and molecular quantum crystals

NASA Astrophysics Data System (ADS)

Cazorla, Claudio; Boronat, Jordi

2017-07-01

Quantum crystals abound in the whole range of solid-state species. Below a certain threshold temperature the physical behavior of rare gases (He 4 and Ne), molecular solids (H2 and CH4 ), and some ionic (LiH), covalent (graphite), and metallic (Li) crystals can be explained only in terms of quantum nuclear effects (QNE). A detailed comprehension of the nature of quantum solids is critical for achieving progress in a number of fundamental and applied scientific fields such as planetary sciences, hydrogen storage, nuclear energy, quantum computing, and nanoelectronics. This review describes the current physical understanding of quantum crystals formed by atoms and small molecules, as well as the wide palette of simulation techniques that are used to investigate them. Relevant aspects in these materials such as phase transformations, structural properties, elasticity, crystalline defects, and the effects of reduced dimensionality are discussed thoroughly. An introduction to quantum Monte Carlo techniques, which in the present context are the simulation methods of choice, and other quantum simulation approaches (e.g., path-integral molecular dynamics and quantum thermal baths) is provided. The overarching objective of this article is twofold: first, to clarify in which crystals and physical situations the disregard of QNE may incur in important bias and erroneous interpretations. And second, to promote the study and appreciation of QNE, a topic that traditionally has been treated in the context of condensed matter physics, within the broad and interdisciplinary areas of materials science.

Physical principles for scalable neural recording

PubMed Central

Zamft, Bradley M.; Maguire, Yael G.; Shapiro, Mikhail G.; Cybulski, Thaddeus R.; Glaser, Joshua I.; Amodei, Dario; Stranges, P. Benjamin; Kalhor, Reza; Dalrymple, David A.; Seo, Dongjin; Alon, Elad; Maharbiz, Michel M.; Carmena, Jose M.; Rabaey, Jan M.; Boyden, Edward S.; Church, George M.; Kording, Konrad P.

2013-01-01

Simultaneously measuring the activities of all neurons in a mammalian brain at millisecond resolution is a challenge beyond the limits of existing techniques in neuroscience. Entirely new approaches may be required, motivating an analysis of the fundamental physical constraints on the problem. We outline the physical principles governing brain activity mapping using optical, electrical, magnetic resonance, and molecular modalities of neural recording. Focusing on the mouse brain, we analyze the scalability of each method, concentrating on the limitations imposed by spatiotemporal resolution, energy dissipation, and volume displacement. Based on this analysis, all existing approaches require orders of magnitude improvement in key parameters. Electrical recording is limited by the low multiplexing capacity of electrodes and their lack of intrinsic spatial resolution, optical methods are constrained by the scattering of visible light in brain tissue, magnetic resonance is hindered by the diffusion and relaxation timescales of water protons, and the implementation of molecular recording is complicated by the stochastic kinetics of enzymes. Understanding the physical limits of brain activity mapping may provide insight into opportunities for novel solutions. For example, unconventional methods for delivering electrodes may enable unprecedented numbers of recording sites, embedded optical devices could allow optical detectors to be placed within a few scattering lengths of the measured neurons, and new classes of molecularly engineered sensors might obviate cumbersome hardware architectures. We also study the physics of powering and communicating with microscale devices embedded in brain tissue and find that, while radio-frequency electromagnetic data transmission suffers from a severe power–bandwidth tradeoff, communication via infrared light or ultrasound may allow high data rates due to the possibility of spatial multiplexing. The use of embedded local recording and wireless data transmission would only be viable, however, given major improvements to the power efficiency of microelectronic devices. PMID:24187539

An Integrated, Statistical Molecular Approach to the Physical Chemistry Curriculum

ERIC Educational Resources Information Center

Cartier, Stephen F.

2009-01-01

As an alternative to the "thermodynamics first" or "quantum first" approaches to the physical chemistry curriculum, the statistical definition of entropy and the Boltzmann distribution are introduced in the first days of the course and the entire two-semester curriculum is then developed from these concepts. Once the tools of statistical mechanics…

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

PubMed Central

2016-01-01

Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of simulation packages, it is anticipated that use of these more complex physical models will lead to new and important discoveries of the physical forces driving a range of chemical and biological phenomena. PMID:26815602

The origami of life

NASA Astrophysics Data System (ADS)

Lezon, Timothy R.; Banavar, Jayanth R.; Maritan, Amos

2006-01-01

All living organisms rely upon networks of molecular interactions to carry out their vital processes. In order for a molecular system to display the properties of life, its constituent molecules must themselves be endowed with several features: stability, specificity, self-organization, functionality, sensitivity, robustness, diversity and adaptability. We argue that these are the emergent properties of a unique phase of matter, and we demonstrate that proteins, the functional molecules of terrestrial life, are perfectly suited to this phase. We explore, through an understanding of this phase of matter, the physical principles that govern the operation of living matter. Our work has implications for the design of functionally useful nanoscale devices and the ultimate development of physically based artificial life.

Physical vapor deposition as a route to glasses with liquid crystalline order

NASA Astrophysics Data System (ADS)

Gomez, Jaritza

Physical vapor deposition (PVD) is an effective route to prepare glasses with a unique combination of properties. Substrate temperatures near the glass transition (Tg) and slow deposition rates can access enhanced mobility at the surface of the glass allowing molecules at the surface additional time to sample different molecular configurations. The temperature of the substrate can be used to control molecular mobility during deposition and properties in the resulting glasses such as higher density, kinetic stability and preferential molecular orientation. PVD was used to prepare glasses of itraconazole, a smectic A liquid crystal. We characterized molecular orientation using infrared and ellipsometry. Molecular orientation can be controlled by choice of Tsubstrate in a range of temperatures near Tg. Glasses deposited at Tsubstrate = Tg show nearly vertical molecular orientation relative to the substrate; at lower Tsubstrate, molecules are nearly parallel to the substrate. The molecular orientation depends on the temperature of the substrate during preparation and not on the molecular orientation of the underlying layer. This allows preparing samples of layers with differing orientations. We find these glasses are homogeneous solids without evidence of domain boundaries and are molecularly flat. We interpret the combination of properties obtained for vapor-deposited glasses of itraconazole to result from a process where molecular orientation is determined by the structure and dynamics at the free surface of the glass during deposition. We report the thermal and structural properties of glasses prepared using PVD of a rod-like molecule, posaconazole, which does not show equilibrium liquid crystal phases. These glasses show substantial molecular orientation that can be controlled by choice of Tsubstrate during deposition. Ellipsometry and IR indicate that glasses prepared at Tg - 3 K are highly ordered. At these Tsubstrate, molecules show preferential vertical orientation and orientation is similar to that measured in aligned nematic liquid crystal. Our results are consistent with a recently proposed mechanism where molecular orientation in equilibrium liquids can be trapped in PVD glasses and suggest that the orientation at the free surface of posaconazole is nematic-like. In addition, we show posaconazole glasses show high kinetic stability controlled by Tsubstrate.

International Conference on Vacuum Ultraviolet Radiation Physics, 8th, Lunds Universitet, Sweden, Aug. 4-8, 1986, Proceedings

NASA Technical Reports Server (NTRS)

Nilsson, Per-Olof (Editor); Nordgren, Joseph (Editor)

1987-01-01

The interactions of VUV radiation with solids are explored in reviews and reports of recent theoretical and experimental investigations from the fields of atomic and molecular physics, solid-state physics, and VUV instrumentation. Topics examined include photoabsorption and photoionization, multiphoton processes, plasma physics, VUV lasers, time-resolved spectroscopy, synchrotron radiation centers, solid-state spectroscopy, and dynamical processes involving localized levels. Consideration is given to the fundamental principles of photoemission, spin-polarized photoemission, inverse photoemission, semiconductors, organic materials, and adsorbates.

1976 annual summary report

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

Not Available

1978-03-01

Abstracts of papers published during the previous calendar year, arranged in accordance with the project titles used in the USDOE Schedule 189 Budget Proposals, are presented. The collection of abstracts supplements the listing of papers published in the Schedule 189. The following subject areas are represented: high-energy physics; nuclear physics; basic energy sciences (nuclear science, materials sciences, solid state physics, materials chemistry); molecular, mathematical, and earth sciences (fundamental interactions, processes and techniques, mathematical and computer sciences); environmental research and development; physical and technological studies (characterization, measurement and monitoring); and nuclear research and applications.

Mirrored continuum and molecular scale simulations of the ignition of gamma phase RDX

NASA Astrophysics Data System (ADS)

Stewart, D. Scott; Chaudhuri, Santanu; Joshi, Kaushik; Lee, Kibaek

2017-01-01

We describe the ignition of an explosive crystal of gamma-phase RDX due to a thermal hot spot with reactive molecular dynamics (RMD), with first-principles trained, reactive force field based molecular potentials that represents an extremely complex reaction network. The RMD simulation is analyzed by sorting molecular product fragments into high and low molecular weight groups, to represent identifiable components that can be interpreted by a continuum model. A continuum model based on a Gibbs formulation has a single temperature and stress state for the mixture. The continuum simulation that mirrors the atomistic simulation allows us to study the atomistic simulation in the familiar physical chemistry framework and provides an essential, continuum/atomistic link.

Astrochemistry at the Cryogenic Storage Ring

NASA Astrophysics Data System (ADS)

Kreckel, Holger; Becker, Arno; Blaum, Klaus; Breitenfeldt, Christian; George, Sebastian; Göck, Jürgen; Grieser, Manfred; Grussie, Florian; Guerin, Elisabeth; Heber, Oded; Karthein, Jonas; Krantz, Claude; Meyer, Christian; Mishra, Preeti; Novotny, Oldrich; O'Connor, Aodh; Saurabh, Sunny; Schippers, Stefan; Spruck, Kaija; Kumar, S. Sunil; Urbain, Xavier; Vogel, Stephen; von Hahn, Robert; Wilhelm, Patrick; Wolf, Andreas; Zajfman, Daniel

2017-01-01

Almost 200 different molecular species have been identified in space, and this number continues to grow steadily. This surprising molecular diversity bears witness to an active reaction network, in which molecular ions are the main drivers of chemistry in the gas phase. To study these reactions under controlled conditions in the laboratory is a major experimental challenge. The new Cryogenic Storage Ring (CSR) that has recently been commissioned at the Max Planck Institute for Nuclear Physics in Heidelberg will serve as an ideal testbed to study cold molecular ions in the gas phase. With residual gas densities of <140 cm-3 and temperatures below 10K, the CSR will allow for merged beams collision studies involving molecular ions, neutral atoms, free electrons and photons under true interstellar conditions.

Preface: Special Topic on Frontiers in Molecular Scale Electronics

NASA Astrophysics Data System (ADS)

Evers, Ferdinand; Venkataraman, Latha

2017-03-01

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

EDITORIAL: Physical Biology

NASA Astrophysics Data System (ADS)

Roscoe, Jane

2004-06-01

Physical Biology is a new peer-reviewed publication from Institute of Physics Publishing. Launched in 2004, the journal will foster the integration of biology with the traditionally more quantitative fields of physics, chemistry, computer science and other math-based disciplines. Its primary aim is to further the understanding of biological systems at all levels of complexity, ranging from the role of structure and dynamics of a single molecule to cellular networks and organisms. The journal encourages the development of a new biology-driven physics based on the extraordinary and increasingly rich data arising in biology, and provides research directions for those involved in the creation of novel bio-engineered systems. Physical Biology will publish a stimulating combination of full length research articles, communications, perspectives, reviews and tutorials from a wide range of disciplines covering topics such as: Single-molecule studies and nanobiotechnology Molecular interactions and protein folding Charge transfer and photobiology Ion channels; structure, function and ion regulation Molecular motors and force generation Subcellular processes Biological networks and neural systems Modeling aspects of molecular and cell biology Cell-cell signaling and interaction Biological patterns and development Evolutionary processes Novel tools and methods in physical biology Experts in the areas encompassed by the journal's scope have been appointed to the Editorial Scientific Committee and the composition of the Committee will be updated regularly to reflect the developments in this new and exciting field. Physical Biology is free online to everyone in 2004; you are invited to take advantage of this offer by visiting the journal homepage at http://physbio.iop.org This special print edition of Physical Biology is a combination of issues 1 and 2 of this electronic-only journal and it brings together an impressive range of articles in the fields covered, including a popular tutorial `An introduction to cell motility for the physical scientist' by D A Fletcher and J A Theriot. Physical Biology offers a number of benefits to the author including free publication (no page or color charges), free multimedia enhancements, rapid publication and a large international readership. To ensure that Physical Biology is truly interdisciplinary and accessible to readers across a broad range of fields, the journal ultilizes a style editor. This unique service makes the journal indispensible to biologists and physicists alike. The feedback from both readers and authors on the use of style editing has been positive: `it is unusual in my experience for a journal to provide such guidance and it augurs well for Physical Biology's role in bridging the gap between the physical and biological sciences' S S Andrews, Lawrence Berkeley Laboratory, USA. You are invited to join the growing list of authors by submitting your work to this new, cutting-edge and rigorously peer-reviewed journal.

1.0 Mm Maps and Radial Density Distributions of Southern Hii/molecular Cloud Complexes

NASA Technical Reports Server (NTRS)

Cheung, L. H.; Frogel, J. A.; Gezar, D. Y.; Hauser, M. G.

1980-01-01

Several 1.0 continuum mapping observations were made of seven southern hemisphere h12/molecular cloud complexes with 65 arcsec resolution. The radial density distribution of the clouds with central luminosity sources was determined observationally. Strong similarities in morphology and general physical conditions were found to exist among all of the southern clouds in the sample.

Introduction to Computational Chemistry: Teaching Hu¨ckel Molecular Orbital Theory Using an Excel Workbook for Matrix Diagonalization

ERIC Educational Resources Information Center

Litofsky, Joshua; Viswanathan, Rama

2015-01-01

Matrix diagonalization, the key technique at the heart of modern computational chemistry for the numerical solution of the Schrödinger equation, can be easily introduced in the physical chemistry curriculum in a pedagogical context using simple Hückel molecular orbital theory for p bonding in molecules. We present details and results of…

Exploring the Nature of the H[subscript 2] Bond. 1. Using Spreadsheet Calculations to Examine the Valence Bond and Molecular Orbital Methods

ERIC Educational Resources Information Center

Halpern, Arthur M.; Glendening, Eric D.

2013-01-01

A three-part project for students in physical chemistry, computational chemistry, or independent study is described in which they explore applications of valence bond (VB) and molecular orbital-configuration interaction (MO-CI) treatments of H[subscript 2]. Using a scientific spreadsheet, students construct potential-energy (PE) curves for several…

Laser Physics and Laser Techniques.

DTIC Science & Technology

1980-02-01

excited states is IGNFACTE produced in a pentacene -doped p-terphenyl molecular crystal by SIGNAL optical absorption from two crossed time-coincident...induces coherent microwave acoustic phonons. These in turn modulate, at the sound frequency, the optical absorption properties of the pentacene molecules... pentacene fects in molecular crystals, and particularly the observa- in p-terphenyl has thus been obtained [2]. tion of an acoustooptic amplitude

Effects of Acute Oral 5-aminotetrazole (5-AT) Exposure to Rats (Rattus norvegicus)

DTIC Science & Technology

2015-02-12

Physical State White crystals White to light yellow crystals Molecular formula CH3N5 CH3N5 · H2O Molecular weight (g/mol) 85.06 103.08 Solubility 12 g/L...Reported to Management/SD Acute Study - Test System Receipt, Facilities, Husbandry, Veterinary Care and Enrichment. 08/15/2013 08/22/2013 Acute Study

Dislocation Onset and Glide in Carbon Nanotubes under Torsion

NASA Astrophysics Data System (ADS)

Dumitrica, Traian; Zhang, Dong-Bo; James, Richard

2009-03-01

The torsional plastic response of carbon nanotubes is comprehensively described in the objective molecular dynamics framework [1-3]. It is shown that an (n,m) tube is prone to slip along a nearly-axial helical path, which introduces a distinct (+1,-1) change in the wrapping index. The low energy realization occurs without loss of mass, via nucleation of a 5-7-7-5 dislocation dipole, followed by a nearly-axial glide of the 5-7 dislocation. The onset of plasticity depends not only on chirality but also on handedness. For a given handedness of the applied twist, chiral tubes of opposed handedness are most susceptible to yield. A right-handed applied twist on an armchair (zig-zag) tube leads to a right- (left-) handed tube. [4pt] [1] T. Dumitrica and R.D. James, Objective Molecular Dynamics, Journal of the Mechanics and Physics of Solids 55, 2206 (2007). [0pt] [2] D.-B. Zhang, M. Hua, and T. Dumitrica, Stability of Polycrystalline and Wurtzite Si Nanowires via Symmetry-Adapted Tight-Binding Objective Molecular Dynamics, Journal of Chemical Physics 128, 084104 (2008). [0pt] [3] D.-B. Zhang and T. Dumitrica, Elasticity of Ideal Single-Walled Carbon Nanotubes via Symmetry-Adapted Tight-Binding Objective Modeling, Applied Physics Letters 93, 031919 (2008).

Physical stability enhancement of theophylline via cocrystallization.

PubMed

Trask, Andrew V; Motherwell, W D Sam; Jones, William

2006-08-31

The crystal form adopted by the respiratory drug theophylline was modified using a crystal engineering strategy in order to search for a solid material with improved physical stability. Cocrystals, also referred to as crystalline molecular complexes, were prepared with theophylline and one of several dicarboxylic acids. Four cocrystals of theophylline are reported, one each with oxalic, malonic, maleic and glutaric acids. Crystal structures were obtained for each cocrystal material, allowing an examination of the hydrogen bonding and crystal packing features. The cocrystal design scheme was partly based upon a series of recently reported cocrystals of the molecular analogue, caffeine, and comparisons in packing features are drawn between the two cocrystal series. The theophylline cocrystals were subjected to relative humidity challenges in order to assess their stability in relation to crystalline theophylline anhydrate and the equivalent caffeine cocrystals. None of the cocrystals in this study converted into a hydrated cocrystal upon storage at high relative humidity. Furthermore, the theophylline:oxalic acid cocrystal demonstrated superior humidity stability to theophylline anhydrate under the conditions examined, while the other cocrystals appeared to offer comparable stability to that of theophylline anhydrate. The results demonstrate the feasibility of pharmaceutical cocrystal design based upon the crystallization preferences of a molecular analogue, and furthermore show that avoidance of hydrate formation and improvement in physical stability is possible via pharmaceutical cocrystallization.

The Effects of Polymer Carrier, Hot Melt Extrusion Process and Downstream Processing Parameters on the Moisture Sorption Properties of Amorphous Solid Dispersions

PubMed Central

Feng, Xin; Vo, Anh; Patil, Hemlata; Tiwari, Roshan V.; Alshetaili, Abdullah S.; Pimparade, Manjeet B.; Repka, Michael A.

2017-01-01

Objective The aim of this study was to evaluate the effect of polymer carrier, hot melt extrusion (HME) and downstream processing parameters on the water uptake properties of amorphous solid dispersions. Methods Three polymers and a model drug were used to prepare amorphous solid dispersions utilizing HME technology. The sorption-desorption isotherms of solid dispersions and their physical mixtures were measured by the Dynamic Vapor Sorption system, and the effect of polymer hydrophobicity, hygroscopicity, molecular weight and the HME process were investigated. FTIR imaging was performed to understand the phase separation driven by the moisture. Key findings Solid dispersions with polymeric carriers with lower hydrophilicity, hygroscopicity, and higher molecular weight could sorb less moisture under the high RH conditions. The water uptake ability of polymer-drug solid dispersion systems were decreased compared to the physical mixture after HME, which might be due to the decreased surface area and porosity. The FTIR imaging indicated the homogeneity of the drug molecularly dispersed within the polymer matrix was changed after exposure to high RH. Conclusion Understanding the effect of formulation and processing on the moisture sorption properties of solid dispersions is essential for the development of drug products with desired physical and chemical stability. PMID:26589107

Dynamic molecular structure of plant biomass-derived black carbon (biochar)

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

Keiluweit, M.; Nico, P.S.; Johnson, M.G.

2009-11-15

Char black carbon (BC), the solid residue of incomplete combustion, is continuously being added to soils and sediments due to natural vegetation fires, anthropogenic pollution, and new strategies for carbon sequestration ('biochar'). Here we present a molecular-level assessment of the physical organization and chemical complexity of biomass-derived chars and, specifically, that of aromatic carbon in char structures. BET-N{sub 2} surface area, X-ray diffraction (XRD), synchrotron-based Near-edge X-ray Absorption Fine Structure (NEXAFS), and Fourier transform infrared (FT-IR) spectroscopy are used to show how two plant materials (wood and grass) undergo analogous, but quantitatively different physical-chemical transitions as charring temperature increases frommore » 100 to 700 C. These changes suggest the existence of four distinct categories of char consisting of a unique mixture of chemical phases and physical states: (i) in transition chars the crystalline character of the precursor materials is preserved, (ii) in amorphous chars the heat-altered molecules and incipient aromatic polycondensates are randomly mixed, (iii) composite chars consist of poorly ordered graphene stacks embedded in amorphous phases, and (iv) turbostratic chars are dominated by disordered graphitic crystallites. The molecular variations among the different char categories translate into differences in their ability to persist in the environment and function as environmental sorbents.« less

Recrystallization of nifedipine and felodipine from amorphous molecular level solid dispersions containing poly(vinylpyrrolidone) and sorbed water.

PubMed

Marsac, Patrick J; Konno, Hajime; Rumondor, Alfred C F; Taylor, Lynne S

2008-03-01

To compare the physical stability of amorphous molecular level solid dispersions of nifedipine and felodipine, in the presence of poly(vinylpyrrolidone) (PVP) and small amounts of moisture. Thin amorphous films of nifedipine and felodipine and amorphous molecular level solid dispersions with PVP were stored at various relative humidities (RH) and the nucleation rate was measured. The amount of water sorbed at each RH was measured using isothermal vapor sorption and glass transition temperatures (Tg) were determined using differential scanning calorimetry. The solubility of each compound in methyl pyrrolidone was measured as a function of water content. Nifedipine crystallizes more easily than felodipine at any given polymer concentration and in the presence of moisture. The glass transition temperatures of each compound, alone and in the presence of PVP, are statistically equivalent at any given water content. The nifedipine systems are significantly more hygroscopic than the corresponding felodipine systems. Variations in the physical stability of the two compounds could not be explained by differences in Tg. However, the relative physical stability is consistent with differences in the degree of supersaturation of each drug in the solid dispersion, treating the polymer and water as a co-solvent system for each drug compound.

Model for diffuse interstellar clouds: improvements to the theory of molecular hydrogen photodestruction and to the gas phase chemistry of carbon monoxide

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

Federman, S.R.

1979-01-01

A theoretical model has been developed to determine physical processes in conjunction with astrophysical observation. The calculations are based on isobaric, steady-state, plane-parallel conditions. In the model, the cloud is illuminated by ultraviolet radiation from one side. The density and temperature of the gas are derived by invoking energy conservation in terms of thermal balance. The derived values for density and temperature then are used to determine the abundances of approximately fifty atomic and molecular species, including important ionic species and simple carbon and oxygen bearing molecules. Except for molecular hydrogen formation on dust grains, binary gas phase reactions aremore » used to develop the chemistry of the model cloud. The theoretical model has been found to be appropriate for a particular range of physical parameters. The results of the steady-state calculations have been compared to ultraviolet observations, predominantly those made with the Copernicus satellite. The theory of molecular hydrogen photodestruction has been reexamined so that improvements to the model can be made. By analyzing the region where the atomic to molecuar hydrogen transition occurs, several processes have been found to contribute to dissociation.« less

Intentions and actions in molecular self-assembly: perspectives on students' language use

NASA Astrophysics Data System (ADS)

Höst, Gunnar E.; Anward, Jan

2017-04-01

Learning to talk science is an important aspect of learning to do science. Given that scientists' language frequently includes intentions and purposes in explanations of unobservable objects and events, teachers must interpret whether learners' use of such language reflects a scientific understanding or inaccurate anthropomorphism and teleology. In the present study, a framework consisting of three 'stances' (Dennett, 1987) - intentional, design and physical - is presented as a powerful tool for analysing students' language use. The aim was to investigate how the framework can be differentiated and used analytically for interpreting students' talk about a molecular process. Semi-structured group discussions and individual interviews about the molecular self-assembly process were conducted with engineering biology/chemistry (n = 15) and biology/chemistry teacher students (n = 6). Qualitative content analysis of transcripts showed that all three stances were employed by students. The analysis also identified subcategories for each stance, and revealed that intentional language with respect to molecular movement and assumptions about design requirements may be potentially problematic areas. Students' exclusion of physical stance explanations may indicate literal anthropomorphic interpretations. Implications for practice include providing teachers with a tool for scaffolding their use of metaphorical language and for supporting students' metacognitive development as scientific language users.

Lighting Up the Force: Investigating Mechanisms of Mechanotransduction Using Fluorescent Tension Probes

PubMed Central

Jurchenko, Carol

2015-01-01

The ability of cells to sense the physical nature of their surroundings is critical to the survival of multicellular organisms. Cellular response to physical cues from adjacent cells and the extracellular matrix leads to a dynamic cycle in which cells respond by remodeling their local microenvironment, fine-tuning cell stiffness, polarity, and shape. Mechanical regulation is important in cellular development, normal morphogenesis, and wound healing. The mechanisms by which these finely balanced mechanotransduction events occur, however, are not well understood. In large part, this is due to the limited availability of tools to study molecular mechanotransduction events in live cells. Several classes of molecular tension probes have been recently developed which are rapidly transforming the study of mechanotransduction. Molecular tension probes are primarily based on fluorescence resonance energy transfer (FRET) and report on piconewton scale tension events in live cells. In this minireview, we describe the two main classes of tension probes, genetically encoded tension sensors and immobilized tension sensors, and discuss the advantages and limitations of each type. We discuss future opportunities to address major biological questions and outline the challenges facing the next generation of molecular tension probes. PMID:26031334

Probing Massive Star Cluster Formation with ALMA

NASA Astrophysics Data System (ADS)

Johnson, Kelsey

2015-08-01

Observationally constraining the physical conditions that give rise to massive star clusters has been a long-standing challenge. Now with the ALMA Observatory coming on-line, we can finally begin to probe the birth environments of massive clusters in a variety of galaxies with sufficient angular resolution. In this talk I will give an overview of ALMA observations of galaxies in which candidate proto-super star cluster molecular clouds have been identified. These new data probe the physical conditions that give rise to super star clusters, providing information on their densities, pressures, and temperatures. In particular, the observations indicate that these clouds may be subject to external pressures of P/k > 108 K cm-3, which is consistent with the prevalence of optically observed adolescent super star clusters in interacting galaxy systems and other high pressure environments. ALMA observations also enable an assessement of the molecular cloud chemical abundances in the regions surrounding super star clusters. Molecular clouds associated with existing super star clusters are strongly correlated with HCO+ emission, but appear to have relatively low ratio of CO/HCO+ emission compared to other clouds, indicating that the super star clusters are impacting the molecular abundances in their vicinity.

Vibrational, NMR and UV-visible spectroscopic investigation and NLO studies on benzaldehyde thiosemicarbazone using computational calculations

NASA Astrophysics Data System (ADS)

Moorthy, N.; Prabakar, P. C. Jobe; Ramalingam, S.; Pandian, G. V.; Anbusrinivasan, P.

2016-04-01

In order to investigate the vibrational, electronic and NLO characteristics of the compound; benzaldehyde thiosemicarbazone (BTSC), the XRD, FT-IR, FT-Raman, NMR and UV-visible spectra were recorded and were analysed with the calculated spectra by using HF and B3LYP methods with 6-311++G(d,p) basis set. The XRD results revealed that the stabilized molecular systems were confined in orthorhombic unit cell system. The cause for the change of chemical and physical properties behind the compound has been discussed makes use of Mulliken charge levels and NBO in detail. The shift of molecular vibrational pattern by the fusing of ligand; thiosemicarbazone group with benzaldehyde has been keenly observed. The occurrence of in phase and out of phase molecular interaction over the frontier molecular orbitals was determined to evaluate the degeneracy of the electronic energy levels. The thermodynamical studies of the temperature region 100-1000 K to detect the thermal stabilization of the crystal phase of the compound were investigated. The NLO properties were evaluated by the determination of the polarizability and hyperpolarizability of the compound in crystal phase. The physical stabilization of the geometry of the compound has been explained by geometry deformation analysis.

Physical properties and scaling relations of molecular clouds: the effect of stellar feedback

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

Tunable Solid State Lasers Based on Molecular Ions

DTIC Science & Technology

1992-01-01

02215 July 15, 1988 to September 30, 1991. N’ o ~...... 1 C~~ I -- ,t,’**, "> I : tt : o0.’. * On leave from Institute of Physics, Copernicus ...Physics, N. Copernicus University, ments provided the ratio (Jo- 81)/10, where l0 is the 87-100 Toruo, Poland. probe beam intensity after passing through...luminescence, following t 30 ns long excitation pulse (308 nm On leave from Institute of Physics, N. Copernicus University, line, excimer laser

The Building Blocks of Materials: Gathering Knowledge at the Molecular Level

NASA Technical Reports Server (NTRS)

2003-01-01

Two start-up positions were created within SD46 to pursue developments in the rapidly expanding areas of biomineralization and nano-technology. As envisioned by Dr. Sandor Lehoczy, the new laboratories to be developed must have the capacity to investigate not only processes associated with the self-assembly of molecules but also the examination of self-assembled structures. For these purposes, laboratories capable of performing the intended function, particularly light scattering spectroscopy and atomic force microscopy were created. What follows then are recent advances arising from the development of these new laboratories. With the implementation of the Atomic Force Microscopy Facility, examples of investigations that determine a correlation between the molecular structure of materials and their macroscopic physical properties are provided. In addition, examples of investigations with particular emphasis on the physical properties of protein crystals, at the molecular level, and subsequent macroscopic characteristics are as provided. Finally, progress in fabrication of technology at the nano-scale levels at the developmental stage is also presented.

Solid surface vs. liquid surface: nanoarchitectonics, molecular machines, and DNA origami.

PubMed

Ariga, Katsuhiko; Mori, Taizo; Nakanishi, Waka; Hill, Jonathan P

2017-09-13

The investigation of molecules and materials at interfaces is critical for the accumulation of new scientific insights and technological advances in the chemical and physical sciences. Immobilization on solid surfaces permits the investigation of different properties of functional molecules or materials with high sensitivity and high spatial resolution. Liquid surfaces also present important media for physicochemical innovation and insight based on their great flexibility and dynamicity, rapid diffusion of molecular components for mixing and rearrangements, as well as drastic spatial variation in the prevailing dielectric environment. Therefore, a comparative discussion of the relative merits of the properties of materials when positioned at solid or liquid surfaces would be informative regarding present-to-future developments of surface-based technologies. In this perspective article, recent research examples of nanoarchitectonics, molecular machines, DNA nanotechnology, and DNA origami are compared with respect to the type of surface used, i.e. solid surfaces vs. liquid surfaces, for future perspectives of interfacial physics and chemistry.

Study on photon transport problem based on the platform of molecular optical simulation environment.

PubMed

Peng, Kuan; Gao, Xinbo; Liang, Jimin; Qu, Xiaochao; Ren, Nunu; Chen, Xueli; Ma, Bin; Tian, Jie

2010-01-01

As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE) to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC) method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (SP(n)), and physical measurement to verify the performance of our study method on both accuracy and efficiency.

Study on Photon Transport Problem Based on the Platform of Molecular Optical Simulation Environment

PubMed Central

Peng, Kuan; Gao, Xinbo; Liang, Jimin; Qu, Xiaochao; Ren, Nunu; Chen, Xueli; Ma, Bin; Tian, Jie

2010-01-01

As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE) to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC) method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (S P n), and physical measurement to verify the performance of our study method on both accuracy and efficiency. PMID:20445737

The ATCA CABB Line Survey on Centaurus A: Properties of the Molecular Gas from the Dust Lanes to the Central Engine

NASA Astrophysics Data System (ADS)

Ott, Juergen; Koribalski, Baerbel; Henkel, Christian; Edwards, Philip; Norris, Ray; Meier, David; Feain, Ilana; Curran, Steve; Martin-Pintado, Jesus; Beelen, Alexandre; Aalto, Susanne; Combes, Francoise; Israel, Frank; Muller, Sebastien; Espada, Daniel; Guelin, Michel; Black, John Harry; V-Trung, Dinh; Impellizzeri, Caterina M. V.; Persson, Carina

2011-10-01

Centaurus A with its host NGC5128 is the most nearby radio galaxy. Its molecular spectrum exhibits three prominent features: a) gas that is located in the outer disk and dust lanes, b) absorption lines that are supposedly close to the central AGN, and c) gas in emission from the nucleus. We propose to perform an extensive line survey toward CenA using the exciting new capabilities of CABB. The broad basebands and narrow zoom bands of CABB are ideal to capture the full breath of the CenA spectral features. Our multi-band line observations will allow us to derive the exact physical conditions of each component as well as the chemistry involved. We will therefore obtain a comprehensive view of the physics imprinted on the molecular spectrum of a radio galaxy and its host, reaching from the central supermassive black hole, through the accretion region and the inner disk to the outer dust lanes.

Many-body expansion of the Fock matrix in the fragment molecular orbital method

NASA Astrophysics Data System (ADS)

Fedorov, Dmitri G.; Kitaura, Kazuo

2017-09-01

A many-body expansion of the Fock matrix in the fragment molecular orbital method is derived up to three-body terms for restricted Hartree-Fock and density functional theory in the atomic orbital basis and compared to the expansion in the basis of fragment molecular orbitals (MOs). The physical nature of many-body corrections is revealed in terms of charge transfer terms. An improvement of the fragment MO expansion is proposed by adding exchange to the embedding. The accuracy of all developed methods is demonstrated in comparison to unfragmented results for polyalanines, a water cluster, Trp-cage (PDB: 1L2Y) and crambin (PDB: 1CRN) proteins, a zeolite cluster, a Si nano-wire, and a boron nitride ribbon. The physical nature of metallicity is discussed, and it is shown what kinds of metallic systems can be treated by fragment-based methods. The density of states is calculated for a fully closed and a partially open nano-ring of boron nitride with a diameter of 105 nm.

Smart Materials Based on DNA Aptamers: Taking Aptasensing to the Next Level

PubMed Central

Mastronardi, Emily; Foster, Amanda; Zhang, Xueru; DeRosa, Maria C.

2014-01-01

“Smart” materials are an emerging category of multifunctional materials with physical or chemical properties that can be controllably altered in response to an external stimulus. By combining the standard properties of the advanced material with the unique ability to recognize and adapt in response to a change in their environment, these materials are finding applications in areas such as sensing and drug delivery. While the majority of these materials are responsive to physical or chemical changes, a particularly exciting area of research seeks to develop smart materials that are sensitive to specific molecular or biomolecular stimuli. These systems require the integration of a molecular recognition probe specific to the target molecule of interest. The ease of synthesis and labeling, low cost, and stability of DNA aptamers make them uniquely suited to effectively serve as molecular recognition probes in novel smart material systems. This review will highlight current work in the area of aptamer-based smart materials and prospects for their future applications. PMID:24553083

Rotational Spectroscopy of Reactive Species at the Center for Astrochemical Studies.

NASA Astrophysics Data System (ADS)

Lattanzi, Valerio; Spezzano, Silvia; Caselli, Paola

2017-06-01

The Center for Astrochemical Studies at the Max Planck Institute for Extraterrestrial Physics in Garching, is a recently established group which collects scientists with very diverse backgrounds. In the same group observers, theoreticians, chemists and molecular astrophysicists join their efforts with the ultimate goal of properly interpreting observations with the new generation telescopes and unveiling our astrochemical/physical heritage. Among these tasks, the gas-phase spectroscopic characterisation of molecular species of astrophysical relevance is one of the main goals of the laboratory sub-group. This talk will mainly focus on the first experiment built in our center, the CASAC (CAS Absorption Cell) spectrometer: this experiment has been optimised on the production and probe of small molecular ions and radicals. The main laboratory techniques along with the more prominent outcomes of recent studies will be presented. Finally, a brief update on the status of the other instruments available in our center will be given, including their planned upgrades.

Computing by physical interaction in neurons.

PubMed

Aur, Dorian; Jog, Mandar; Poznanski, Roman R

2011-12-01

The electrodynamics of action potentials represents the fundamental level where information is integrated and processed in neurons. The Hodgkin-Huxley model cannot explain the non-stereotyped spatial charge density dynamics that occur during action potential propagation. Revealed in experiments as spike directivity, the non-uniform charge density dynamics within neurons carry meaningful information and suggest that fragments of information regarding our memories are endogenously stored in structural patterns at a molecular level and are revealed only during spiking activity. The main conceptual idea is that under the influence of electric fields, efficient computation by interaction occurs between charge densities embedded within molecular structures and the transient developed flow of electrical charges. This process of computation underlying electrical interactions and molecular mechanisms at the subcellular level is dissimilar from spiking neuron models that are completely devoid of physical interactions. Computation by interaction describes a more powerful continuous model of computation than the one that consists of discrete steps as represented in Turing machines.

Electron and Ion Reactions in Molecular Solids: from astrochemistry to radiobiology

NASA Astrophysics Data System (ADS)

Huels, Michael A.

2001-05-01

Wherever ionizing radiation interacts with matter, it initiates reaction cascades involving ions, radicals, and ballistic secondary electrons; these reactions occur on fs time-scales, and may lead to substantial physical and chemical modifications of a medium. Here I present measurements of 0-80 eV electron and ion reactions in condensed films ranging from simple to complex, and astrophysical to biological in nature. Targets contain either: small molecules, hydrocarbons of increasing complexity (incl. bases, sugars, single/double stranded DNA), molecules on rare gas matrices, or mixed cryogenic films resembling astrophysical or planetary surface ices containing O2, H2O, methane, and aromatic hydrocarbons. The basic electron or ion reaction mechanisms and pathways are found to be fundamentally universal, but are modulated by the physical and chemical nature of the medium; depending on the latter, a reaction cascade may lead to different end-points, e.g. a decrease in molecular complexity via molecular fragmentations, or increases in complexity via secondary ion collision induced synthesis of larger molecules in hydrocarbon rich surface ices.

Effect of Chemical and Physical Properties on the In Vitro Degradation of 3D Printed High Resolution Poly(propylene fumarate) Scaffolds.

PubMed

Walker, Jason M; Bodamer, Emily; Krebs, Olivia; Luo, Yuanyuan; Kleinfehn, Alex; Becker, Matthew L; Dean, David

2017-04-10

Two distinct molecular masses of poly(propylene fumarate) (PPF) are combined with an additive manufacturing process to fabricate highly complex scaffolds possessing controlled chemical properties and porous architecture. Scaffolds were manufactured with two polymer molecular masses and two architecture styles. Degradation was assessed in an accelerated in vitro environment. The purpose of the degradation study is not to model or mimic in vivo degradation, but to efficiently compare the effect of modulating scaffold properties. This is the first study addressing degradation of chain-growth synthesized PPF, a process that allows for considerably more control over molecular mass distribution. It demonstrates that, with greater process control, not only is scaffold fabrication reproducible, but the mechanical properties and degradation kinetics can be tailored by altering the physical properties of the scaffold. This is a clear step forward in using PPF to address unmet medical needs while meeting regulatory demands and ultimately obtaining clinical relevancy.

Mathematical modeling of molecular diffusion through mucus

PubMed Central

Cu, Yen; Saltzman, W. Mark

2008-01-01

The rate of molecular transport through the mucus gel can be an important determinant of efficacy for therapeutic agents delivered by oral, intranasal, intravaginal/rectal, and intraocular routes. Transport through mucus can be described by mathematical models based on principles of physical chemistry and known characteristics of the mucus gel, its constituents, and of the drug itself. In this paper, we review mathematical models of molecular diffusion in mucus, as well as the techniques commonly used to measure diffusion of solutes in the mucus gel, mucus gel mimics, and mucosal epithelia. PMID:19135488

A study on the anisole-water complex by molecular beam-electronic spectroscopy and molecular mechanics calculations.

PubMed

Becucci, M; Pietraperzia, G; Pasquini, M; Piani, G; Zoppi, A; Chelli, R; Castellucci, E; Demtroeder, W

2004-03-22

An experimental and theoretical study is made on the anisole-water complex. It is the first van der Waals complex studied by high resolution electronic spectroscopy in which the water is seen acting as an acid. Vibronically and rotationally resolved electronic spectroscopy experiments and molecular mechanics calculations are used to elucidate the structure of the complex in the ground and first electronic excited state. Some internal dynamics in the system is revealed by high resolution spectroscopy. (c) 2004 American Institute of Physics

Instrumentation concepts and requirements for a space vacuum research facility. [molecular shield for spaceborne experiments

NASA Technical Reports Server (NTRS)

Norton, H. N.

1979-01-01

An earth-orbiting molecular shield that offers a unique opportunity for conducting physics, chemistry, and material processing experiments under a combination of environmental conditions that are not available in terrestrial laboratories is equipped with apparatus for forming a molecular beam from the freestream. Experiments are carried out using a moderate energy, high flux density, high purity atomic oxygen beam in the very low density environment within the molecular shield. As a minimum, the following instruments are required for the molecular shield: (1) a mass spectrometer; (2) a multifunction material analysis instrumentation system; and (3) optical spectrometry equipment. The design is given of a furlable molecular shield that allows deployment and retrieval of the system (including instrumentation and experiments) to be performed without contamination. Interfaces between the molecular shield system and the associated spacecraft are given. An in-flight deployment sequence is discussed that minimizes the spacecraft-induced contamination in the vicinity of the shield. Design approaches toward a precursor molecular shield system are shown.

Theoretical and experimental investigations of superconductivity. Amorphous semiconductors, superconductivity and magnetism

NASA Technical Reports Server (NTRS)

Cohen, M. H.

1973-01-01

The research activities from 1 March 1963 to 28 February 1973 are summarized. Major lectures are listed along with publications on superconductivity, superfluidity, electronic structures and Fermi surfaces of metals, optical spectra of solids, electronic structure of insulators and semiconductors, theory of magnetic metals, physics of surfaces, structures of metals, and molecular physics.

Conceptual Integration of Hybridization by Algerian Students Intending to Teach Physical Sciences

ERIC Educational Resources Information Center

Salah, Hazzi; Dumon, Alain

2011-01-01

This work aims to assess the difficulties encountered by students of the Ecole Normale Superieure of Kouba (Algeria) intending to teach physical science in the integration of the hybridization of atomic orbitals. It is a concept that they should use in describing the formation of molecular orbitals ([sigma] and [pi]) in organic chemistry and gaps…

Detailed characterization of mechanical properties and molecular mobility within dry seed glasses: relevance to the physiology of dry biological systems.

PubMed

Ballesteros, Daniel; Walters, Christina

2011-11-01

Slow movement of molecules in glassy matrices controls the kinetics of chemical and physical reactions in dry seeds. Variation in physiological activity among seeds suggests that there are differences in mobility among seed glasses. Testing this hypothesis is difficult because few tools are available to measure molecular mobility within dry seeds. Here, motional properties within dry pea cotyledons were assessed using dynamic mechanical analysis. The technique detected several molecular relaxations between -80 and +80°C and gave a more detailed description of water content-temperature effects on molecular motion than previously understood from studies of glass formation in seeds at glass transition (Tg). Diffusive movement is delimited by the α relaxation, which appears to be analogous to Tg. β and γ relaxations were also detected at temperatures lower than α relaxations, clearly demonstrating intramolecular motion within the glassy matrix of the pea cotyledon. Glass transitions, or the mechanical counterpart α relaxation, appear to be less relevant to seed aging during dry storage than previously thought. On the other hand, β relaxation occurs at temperature and moisture conditions typically used for seed storage and has established importance for physical aging of synthetic polymer glasses. Our data show that the nature and extent of molecular motion varies considerably with moisture and temperature, and that the hydrated conditions used for accelerated aging experiments and ultra-dry conditions sometimes recommended for seed storage give greater molecular mobility than more standard seed storage practices. We believe characterization of molecular mobility is critical for evaluating how dry seeds respond to the environment and persist through time. Published 2011. This article is a US Government work and is in the public domain in the USA.

Triggered massive star formation associated with the bubble Hii region Sh2-39 (N5)

NASA Astrophysics Data System (ADS)

Duronea, N. U.; Cappa, C. E.; Bronfman, L.; Borissova, J.; Gromadzki, M.; Kuhn, M. A.

2017-09-01

Aims: We perform a multiwavelength analysis of the bubble Hii region Sh2-39 (N5) and its environs with the aim of studying the physical properties of Galactic IR bubbles and exploring their impact in triggering massive star formation. Methods: To analyze the molecular gas, we used CO(3-2) and HCO+(4-3) line data obtained with the on-the-fly technique from the ASTE telescope. To study the distribution and physical characteristics of the dust, we made use of archival data from ATLASGAL, Herschel, and MSX, while the ionized gas was studied making use of an NVSS image. We used public WISE, Spitzer, and MSX point source catalogs to search for infrared candidate young stellar objects (YSOs) in the region. To investigate the stellar cluster [BDS2003]6 we used IR spectroscopic data obtained with the ARCoIRIS spectrograph, mounted on Blanco 4 m Telescope at CTIO, and new available IR Ks band observations from the VVVeXtended ESO Public Survey (VVVX). Results: The new ASTE observations allowed the molecular gas component in the velocity range from 30 km s-1 to 46 km s-1, associated with Sh2-39, to be studied in detail. The morphology of the molecular gas suggests that the ionized gas is expanding against its parental cloud. We identified four molecular clumps, which were likely formed by the expansion of the ionization front, and determined some of their physical and dynamical properties. Clumps with HCO+ and 870 μm counterparts show evidence of gravitational collapse. We identified several candidate YSOs across the molecular component. Their spatial distribution and the fragmentation time derived for the collected layers of the molecular gas suggest that massive star formation might have been triggered by the expansion of the nebula via the collect and collapse mechanism. The spectroscopical distance obtained for the stellar cluster [BDS2003]6, placed over one of the collapsing clumps in the border of the Hii region, reveals that this cluster is physically associated with the nebula and gives more support to the triggered massive star formation scenario. A radio continuum data analysis indicates that the nebula is older and expands at lower velocity than typical IR Galactic bubbles. The ASTE data cubes and ARCoIRIS spectrum are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/606/A8

Creating and Using a Consumer Chemical Molecular Graphics Database: The "Molecule of the Day" - A Great Way To Begin Your Lecture

NASA Astrophysics Data System (ADS)

Scharberg, Maureen A.; Cox, Oran E.; Barelli, Carl A.

1997-07-01

"The Molecule of the Day" consumer chemical database has been created to allow introductory chemistry students to explore molecular structures of chemicals in household products, and to provide opportunities in molecular modeling for undergraduate chemistry students. Before class begins, an overhead transparency is displayed which shows a three-dimensional molecular structure of a household chemical, and lists relevant features and uses of this chemical. Within answers to questionnaires, students have commented that this molecular graphics database has helped them to visually connect the microscopic structure of a molecule with its physical and chemical properties, as well as its uses in consumer products. It is anticipated that this database will be incorporated into a navigational software package such as Netscape.

Molecular Electron Density Theory: A Modern View of Reactivity in Organic Chemistry.

PubMed

Domingo, Luis R

2016-09-30

A new theory for the study of the reactivity in Organic Chemistry, named Molecular Electron Density Theory (MEDT), is proposed herein. MEDT is based on the idea that while the electron density distribution at the ground state is responsible for physical and chemical molecular properties, as proposed by the Density Functional Theory (DFT), the capability for changes in electron density is responsible for molecular reactivity. Within MEDT, the reactivity in Organic Chemistry is studied through a rigorous quantum chemical analysis of the changes of the electron density as well as the energies associated with these changes along the reaction path in order to understand experimental outcomes. Studies performed using MEDT allow establishing a modern rationalisation and to gain insight into molecular mechanisms and reactivity in Organic Chemistry.

Prevention of peritoneal adhesions using polymeric rheological blends.

PubMed

Hoare, Todd; Yeo, Yoon; Bellas, Evangelia; Bruggeman, Joost P; Kohane, Daniel S

2014-03-01

The effectiveness of rheological blends of high molecular weight hyaluronic acid (HA) and low molecular weight hydroxypropyl methylcellulose (HPMC) in the prevention of peritoneal adhesions post-surgery is demonstrated. The physical mixture of the two carbohydrates increased the dwell time in the peritoneum while significantly improving the injectability of the polymer compared with HA alone. HA-HPMC treatment decreased the total adhesion area by ∼ 70% relative to a saline control or no treatment in a repeated cecal injury model in the rabbit. No significant cytotoxicity and minimal inflammation were associated with the blend. Furthermore, no chemical or physical processing was required prior to their use beyond simple mixing. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Soot and Spectral Radiation Modeling in ECN Spray A and in Engines

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

Haworth, Daniel C; Ferreyro-Fernandez, Sebastian; Paul, Chandan

The amount of soot formed in a turbulent combustion system is determined by a complex system of coupled nonlinear chemical and physical processes. Different physical subprocesses can dominate, depending on the hydrodynamic and thermochemical environments. Similarly, the relative importance of reabsorption, spectral radiation properties, and molecular gas radiation versus soot radiation varies with thermochemical conditions, and in ways that are difficult to predict for the highly nonhomogeneous in-cylinder mixtures in engines. Here it is shown that transport and mixing play relatively more important roles as rate-determining processes in soot formation at engine-relevant conditions. It is also shown that molecular gasmore » radiation and spectral radiation properties are important for engine-relevant conditions.« less

The development and characterisation of a bacterial artificial chromosome library for Fragaria vesca

PubMed Central

Bonet, Julio; Girona, Elena Lopez; Sargent, Daniel J; Muñoz-Torres, Monica C; Monfort, Amparo; Abbott, Albert G; Arús, Pere; Simpson, David W; Davik, Jahn

2009-01-01

Background The cultivated strawberry Fragaria ×ananassa is one of the most economically-important soft-fruit species. Few structural genomic resources have been reported for Fragaria and there exists an urgent need for the development of physical mapping resources for the genus. The first stage in the development of a physical map for Fragaria is the construction and characterisation of a high molecular weight bacterial artificial chromosome (BAC) library. Methods A BAC library, consisting of 18,432 clones was constructed from Fragaria vesca f. semperflorens accession 'Ali Baba'. BAC DNA from individual library clones was pooled to create a PCR-based screening assay for the library, whereby individual clones could be identified with just 34 PCR reactions. These pools were used to screen the BAC library and anchor individual clones to the diploid Fragaria reference map (FV×FN). Findings Clones from the BAC library developed contained an average insert size of 85 kb, representing over seven genome equivalents. The pools and superpools developed were used to identify a set of BAC clones containing 70 molecular markers previously mapped to the diploid Fragaria FV×FN reference map. The number of positive colonies identified for each marker suggests the library represents between 4× and 10× coverage of the diploid Fragaria genome, which is in accordance with the estimate of library coverage based on average insert size. Conclusion This BAC library will be used for the construction of a physical map for F. vesca and the superpools will permit physical anchoring of molecular markers using PCR. PMID:19772672

The Chromosome Microdissection and Microcloning Technique.

PubMed

Zhang, Ying-Xin; Deng, Chuan-Liang; Hu, Zan-Min

2016-01-01

Chromosome microdissection followed by microcloning is an efficient tool combining cytogenetics and molecular genetics that can be used for the construction of the high density molecular marker linkage map and fine physical map, the generation of probes for chromosome painting, and the localization and cloning of important genes. Here, we describe a modified technique to microdissect a single chromosome, paint individual chromosomes, and construct single-chromosome DNA libraries.

Organic molecules on metal and oxide semiconductor substrates: Adsorption behavior and electronic energy level alignment

NASA Astrophysics Data System (ADS)

Ruggieri, Charles M.

Modern devices such as organic light emitting diodes use organic/oxide and organic/metal interfaces for crucial processes such as charge injection and charge transfer. Understanding fundamental physical processes occurring at these interfaces is essential to improving device performance. The ultimate goal of studying such interfaces is to form a predictive model of interfacial interactions, which has not yet been established. To this end, this thesis focuses on obtaining a better understanding of fundamental physical interactions governing molecular self-assembly and electronic energy level alignment at organic/metal and organic/oxide interfaces. This is accomplished by investigating both the molecular adsorption geometry using scanning tunneling microscopy, as well as the electronic structure at the interface using direct and inverse photoemission spectroscopy, and analyzing the results in the context of first principles electronic structure calculations. First, we study the adsorption geometry of zinc tetraphenylporphyrin (ZnTPP) molecules on three noble metal surfaces: Au(111), Ag(111), and Ag(100). These surfaces were chosen to systematically compare the molecular self-assembly and adsorption behavior on two metals of the same surface symmetry and two surface symmetries of one metal. From this investigation, we improve the understanding of self-assembly at organic/metal interfaces and the relative strengths of competing intermolecular and molecule-substrate interactions that influence molecular adsorption geometry. We then investigate the electronic structure of the ZnTPP/Au(111), Ag(111), and Ag(100) interfaces as examples of weakly-interacting systems. We compare these cases to ZnTPP on TiO2(110), a wide-bandgap oxide semiconductor, and explain the intermolecular and molecule-substrate interactions that determine the electronic energy level alignment at the interface. Finally we study tetracyanoquinodimethane (TCNQ), a strong electron acceptor, on TiO2(110), which exhibits chemical hybridization accompanied by molecular distortion, as well as extreme charge transfer resulting in the development of a space charge layer in the oxide. Thus, we present a broad experimental and theoretical perspective on the study of organic/metal and organic/oxide interfaces, elucidating fundamental physical interactions that govern molecular organization and energy level alignment.

Nuclear chemistry. Annual report, 1974

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

Conzett, H.E.; Edelstein, N.M.; Tsang, C.F.

1975-07-01

The 1974 Nuclear Chemistry Annual Report contains information on research in the following areas: nuclear science (nuclear spectroscopy and radioactivity, nuclear reactions and scattering, nuclear theory); chemical and atomic physics (heavy ion-induced atomic reactions, atomic and molecular spectroscopy, photoelectron spectroscopy and hyperfine interactions); physical, inorganic, and analytical chemistry (x-ray crystallography, physical and inorganic chemistry, geochemistry); and instrumentation. Thesis abstracts, 1974 publication titles, and an author index are also included. Papers having a significant amount of information are listed separately by title. (RWR)

Deriving principles of microbiology by multiscaling laws of molecular physics.

PubMed

Ortoleva, Peter; Adhangale, P; Cheluvaraja, S; Fontus, Max; Shreif, Zeina

2009-01-01

It has long been an objective of the physical sciences to derive principles of biology from the laws of physics. At the angstrom scale for processes evolving on timescales of 10(-14) s, many systems can be characterized in terms of atomic vibrations and collisions. In contrast, biological systems display dramatic transformations including self-assembly and reorganization from one cell phenotype to another as the microenvironment changes. We have developed a framework for understanding the emergence of living systems from the underlying atomic chaos.

The Molecular Mechanism of the Supra-Additive Response of Prostate Cancer to Androgen Ablation and Radiotherapy

DTIC Science & Technology

2001-02-01

being seen approximately every 6 months PAP levels was found (Table 3). Pretreatment PSAs >10 with interval history, physical examination, serum PSA...Aknowledgments-This study was supported in part by Depart- 1507 � I. J. Radiation Oncology 0 Biology @ Physics Volume 48, Number 5, 2000 of hormone...than nonspecific one standard deviation above and below the mean. 1510 I. J. Radiation Oncology 0 Biology 0 Physics Volume 48, Number 5, 2000 significant

A computational chemistry perspective on the current status and future direction of hepatitis B antiviral drug discovery.

PubMed

Morgnanesi, Dante; Heinrichs, Eric J; Mele, Anthony R; Wilkinson, Sean; Zhou, Suzanne; Kulp, John L

2015-11-01

Computational chemical biology, applied to research on hepatitis B virus (HBV), has two major branches: bioinformatics (statistical models) and first-principle methods (molecular physics). While bioinformatics focuses on statistical tools and biological databases, molecular physics uses mathematics and chemical theory to study the interactions of biomolecules. Three computational techniques most commonly used in HBV research are homology modeling, molecular docking, and molecular dynamics. Homology modeling is a computational simulation to predict protein structure and has been used to construct conformers of the viral polymerase (reverse transcriptase domain and RNase H domain) and the HBV X protein. Molecular docking is used to predict the most likely orientation of a ligand when it is bound to a protein, as well as determining an energy score of the docked conformation. Molecular dynamics is a simulation that analyzes biomolecule motions and determines conformation and stability patterns. All of these modeling techniques have aided in the understanding of resistance mutations on HBV non-nucleos(t)ide reverse-transcriptase inhibitor binding. Finally, bioinformatics can be used to study the DNA and RNA protein sequences of viruses to both analyze drug resistance and to genotype the viral genomes. Overall, with these techniques, and others, computational chemical biology is becoming more and more necessary in hepatitis B research. This article forms part of a symposium in Antiviral Research on "An unfinished story: from the discovery of the Australia antigen to the development of new curative therapies for hepatitis B." Copyright © 2015 Elsevier B.V. All rights reserved.

REVIEWS OF TOPICAL PROBLEMS: Application of cybernetic methods in physics

NASA Astrophysics Data System (ADS)

Fradkov, Aleksandr L.

2005-02-01

Basic aspects of the subject and methodology for a new and rapidly developing area of research that has emerged at the intersection of physics and control theory (cybernetics) and emphasizes the application of cybernetic methods to the study of physical systems are reviewed. Speed-gradient and Hamiltonian solutions for energy control problems in conservative and dissipative systems are presented. Application examples such as the Kapitza pendulum, controlled overcoming of a potential barrier, and controlling coupled oscillators and molecular systems are presented. A speed-gradient approach to modeling the dynamics of physical systems is discussed.

Physics at the FMQT’08 conference

NASA Astrophysics Data System (ADS)

Špička, V.; Nieuwenhuizen, Th. M.; Keefe, P. D.

2010-01-01

This paper summarizes the recent state of the art of the following topics presented at the FQMT’08 conference: Foundations of quantum physics, Quantum measurement; Quantum noise, decoherence and dephasing; Cold atoms and Bose-Einstein condensation; Physics of quantum computing and information; Nonequilibrium quantum statistical mechanics; Quantum, mesoscopic and partly classical thermodynamics; Mesoscopic, nano-electro-mechanical systems and optomechanical systems; Spins systems and their dynamics, Brownian motion and molecular motors; Physics of biological systems, and Relevant experiments from the nanoscale to the macroscale. To all these subjects an introduction is given and the recent literature is overviewed. The paper contains some 680 references in total.

An intermediate-level course on Biological Physics

NASA Astrophysics Data System (ADS)

Nelson, Phil

2004-03-01

I describe both undergraduate and graduate 1-semester courses designed to give a survey of Biological Physics. The courses cover classical as well as recent topics. The undergraduate version requires calculus-based first-year physics as its prerequisite. With this level of assumed background, we can arrive at topics such as molecular motors, manipulation of single molecules, and the propagation of nerve impulses. Students majoring in physics, chemistry, biochemistry, and every engineering major (as well as a few in biology), end up taking this course. The graduate course covers the same material but includes exercises with symbolic mathematics packages and data modeling.

Nonunique and nonuniform mapping in few-body Coulomb-explosion imaging

NASA Astrophysics Data System (ADS)

Sayler, A. M.; Eckner, E.; McKenna, J.; Esry, B. D.; Carnes, K. D.; Ben-Itzhak, I.; Paulus, G. G.

2018-03-01

Much of our knowledge of molecular geometry and interaction dynamics comes from indirect measurements of the molecular fragments following breakup. This technique—Coulomb-explosion imaging (CEI), i.e., determining the initial molecular configuration of a system from the momenta of the resulting fragments using knowledge of the particle interactions—is one of the fundamental tools of molecular physics. Moreover, CEI has been a staple of molecular studies for decades. Here we show that one often cannot assign a unique initial configuration to the few-body breakup of a polyatomic molecule given the measurement of the resulting fragments' momenta. Specifically, multiple initial configurations can result in identical momenta for a molecule breaking into three or more parts. Further, the nonunique and nonuniform mapping from the initial configuration to the measured momenta also significantly complicates the determination of molecular alignment at the time of breakup.

Molecular Momentum Transport at Fluid-Solid Interfaces in MEMS/NEMS: A Review

PubMed Central

Cao, Bing-Yang; Sun, Jun; Chen, Min; Guo, Zeng-Yuan

2009-01-01

This review is focused on molecular momentum transport at fluid-solid interfaces mainly related to microfluidics and nanofluidics in micro-/nano-electro-mechanical systems (MEMS/NEMS). This broad subject covers molecular dynamics behaviors, boundary conditions, molecular momentum accommodations, theoretical and phenomenological models in terms of gas-solid and liquid-solid interfaces affected by various physical factors, such as fluid and solid species, surface roughness, surface patterns, wettability, temperature, pressure, fluid viscosity and polarity. This review offers an overview of the major achievements, including experiments, theories and molecular dynamics simulations, in the field with particular emphasis on the effects on microfluidics and nanofluidics in nanoscience and nanotechnology. In Section 1 we present a brief introduction on the backgrounds, history and concepts. Sections 2 and 3 are focused on molecular momentum transport at gas-solid and liquid-solid interfaces, respectively. Summary and conclusions are finally presented in Section 4. PMID:20087458

Reprogrammable Assembly of Molecular Motor on Solid Surfaces via Dynamic Bonds.

PubMed

Yu, Li; Sun, Jian; Wang, Qian; Guan, Yan; Zhou, Le; Zhang, Jingxuan; Zhang, Lanying; Yang, Huai

2017-06-01

Controllable assembly of molecular motors on solid surfaces is a fundamental issue for providing them to perform physical tasks. However, it can hardly be achieved by most previous methods due to their inherent limitations. Here, a general strategy is designed for the reprogrammable assembly of molecular motors on solid surfaces based on dynamic bonds. In this method, molecular motors with disulfide bonds can be remotely, reversibly, and precisely attached to solid surfaces with disulfide bonds, regardless of their chemical composition and microstructure. More importantly, it not only allows encoding geometric information referring to a pattern of molecular motors, but also enables erasing and re-encoding of geometric information via hemolytic photocleavage and recombination of disulfide bonds. Thus, solid surfaces can be regarded as "computer hardware", where molecular motors can be reformatted and reprogramed as geometric information. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of polyacrylamide on soil physical and hydraulic properties

NASA Astrophysics Data System (ADS)

Albalasmeh, Ammar; Gharaibeh, Mamoun; Hamdan, Enas

2017-04-01

The effect of polyacrylamide (PAM), as a soil conditioner, on selected soil physical and hydraulic properties (infiltration rate (f(t)), hydraulic conductivity (HC), soil moisture content, aggregate stability (AS), and soil aggregation) was studied. Two types of anionic PAM were used: Low molecular weight (LPAM) (1×105 g/mol) with medium charge density (33-43) and high molecular weight (HPAM) (1-6×106 g/mol) with medium charge density (33-43). Sandy loam soil was packed into plastic columns; PAM solutions at different concentrations (100, 250, 500, and 1000 mg L-1) were used every two weeks in four wetting and drying cycles. The highest infiltration rate value was 0.16 mm s-1 at 1000 mg/L low molecular weight PAM while the highest value of infiltration rate in high PAM molecular weight was 0.11 mm s-1 compared to the control (0.01 mm s-1). Soil HC was about 3.00 cm h-1 for LPAM at 1000 mg L-1 PAM, while the highest value for HPAM was about 2 cm h-1 for the same concentration, compared to the control. The amount of water that can be held by soil increased with the addition of PAM compared to the control. Differences in water content were more pronounced in LPAM compared to HPAM. The addition of LPAM increased aggregate stability proportional to PAM concentration. Moreover, 1000 mg L-1 produced the highest aggregate stability (19{%}) compared to HPAM and control (7{%} and 5{%}), respectively. As PAM concentration increased, the geometric mean diameter (GMD) increased for both PAM molecular weights compared to control (0.4 mm). At 1000 mg L-1 the GMD values were 0.88 mm and 0.79 mm for LPAM and HPAM, respectively. The addition of PAM improved soil physical and hydraulic properties, with an advantage to LPAM owing that to its ability to penetrate soil aggregates and therefore stabilizing them.

On the vibrational behavior of single- and double-walled carbon nanotubes under the physical adsorption of biomolecules in the aqueous environment: a molecular dynamics study.

PubMed

Ajori, S; Ansari, R; Darvizeh, M

2016-03-01

The adsorption of biomolecules on the walls of carbon nanotubes (CNTs) in an aqueous environment is of great importance in the field of nanobiotechnology. In this study, molecular dynamics (MD) simulations were performed to understand the mechanical vibrational behavior of single- and double-walled carbon nanotubes (SWCNTs and DWCNTs) under the physical adsorption of four important biomolecules (L-alanine, guanine, thymine, and uracil) in vacuum and an aqueous environment. It was observed that the natural frequencies of these CNTs in vacuum reduce under the physical adsorption of biomolecules. In the aqueous environment, the natural frequency of each pure CNT decreased as compared to its natural frequency in vacuum. It was also found that the frequency shift for functionalized CNTs as compared to pure CNTs in the aqueous environment was dependent on the radius and the number of walls of the CNT, and could be positive or negative.

Understanding the Cellular and Molecular Mechanisms of Physical Activity-Induced Health Benefits.

PubMed

Neufer, P Darrell; Bamman, Marcas M; Muoio, Deborah M; Bouchard, Claude; Cooper, Dan M; Goodpaster, Bret H; Booth, Frank W; Kohrt, Wendy M; Gerszten, Robert E; Mattson, Mark P; Hepple, Russell T; Kraus, William E; Reid, Michael B; Bodine, Sue C; Jakicic, John M; Fleg, Jerome L; Williams, John P; Joseph, Lyndon; Evans, Mary; Maruvada, Padma; Rodgers, Mary; Roary, Mary; Boyce, Amanda T; Drugan, Jonelle K; Koenig, James I; Ingraham, Richard H; Krotoski, Danuta; Garcia-Cazarin, Mary; McGowan, Joan A; Laughlin, Maren R

2015-07-07

The beneficial effects of physical activity (PA) are well documented, yet the mechanisms by which PA prevents disease and improves health outcomes are poorly understood. To identify major gaps in knowledge and potential strategies for catalyzing progress in the field, the NIH convened a workshop in late October 2014 entitled "Understanding the Cellular and Molecular Mechanisms of Physical Activity-Induced Health Benefits." Presentations and discussions emphasized the challenges imposed by the integrative and intermittent nature of PA, the tremendous discovery potential of applying "-omics" technologies to understand interorgan crosstalk and biological networking systems during PA, and the need to establish an infrastructure of clinical trial sites with sufficient expertise to incorporate mechanistic outcome measures into adequately sized human PA trials. Identification of the mechanisms that underlie the link between PA and improved health holds extraordinary promise for discovery of novel therapeutic targets and development of personalized exercise medicine. Copyright © 2015 Elsevier Inc. All rights reserved.

Bridging the Gaps: the Promise of Omics Studies in Pediatric Exercise Research

PubMed Central

Radom-Aizik, Shlomit; Cooper, Dan M.

2018-01-01

In this review, we highlight promising new discoveries that may generate useful and clinically relevant insights into the mechanisms that link exercise with growth during critical periods of development. Growth in childhood and adolescence is unique among mammals, and is a dynamic process regulated by an evolution of hormonal and inflammatory mediators, age-dependent progression of gene expression, and environmentally modulated epigenetic mechanisms. Many of these same processes likely affect molecular transducers of physical activity. How the molecular signaling associated with growth is synchronized with signaling associated with exercise is poorly understood. Recent advances in “omics,” namely, genomics and epigenetics, metabolomics, and proteomics, now provide exciting approaches and tools that can be used for the first time to address this gap. A biologic definition of “healthy” exercise that links the metabolic transducers of physical activity with parallel processes that regulate growth will transform health policy and guidelines that promote optimal use of physical activity. PMID:27137166

Remotely controlled fusion of selected vesicles and living cells: a key issue review

NASA Astrophysics Data System (ADS)

Bahadori, Azra; Moreno-Pescador, Guillermo; Oddershede, Lene B.; Bendix, Poul M.

2018-03-01

Remote control over fusion of single cells and vesicles has a great potential in biological and chemical research allowing both transfer of genetic material between cells and transfer of molecular content between vesicles. Membrane fusion is a critical process in biology that facilitates molecular transport and mixing of cellular cytoplasms with potential formation of hybrid cells. Cells precisely regulate internal membrane fusions with the aid of specialized fusion complexes that physically provide the energy necessary for mediating fusion. Physical factors like membrane curvature, tension and temperature, affect biological membrane fusion by lowering the associated energy barrier. This has inspired the development of physical approaches to harness the fusion process at a single cell level by using remotely controlled electromagnetic fields to trigger membrane fusion. Here, we critically review various approaches, based on lasers or electric pulses, to control fusion between individual cells or between individual lipid vesicles and discuss their potential and limitations for present and future applications within biochemistry, biology and soft matter.

Interfacial mixing in high energy-density matter with a multiphysics kinetic model

NASA Astrophysics Data System (ADS)

Haack, Jeff; Hauck, Cory; Murillo, Michael

2017-10-01

We have extended a recently-developed multispecies, multitemperature BGK model to include multiphysics capability that allows modeling of a wider range of plasma conditions. In particular, we have extended the model to describe one spatial dimension, and included a multispecies atomic ionization model, accurate collision physics across coupling regimes, self-consistent electric fields, and degeneracy in the electronic screening. We apply the new model to a warm dense matter scenario in which the ablator-fuel interface of an inertial confinement fusion target is heated, similar to a recent molecular dynamics study, but for larger length and time scales and for much higher temperatures. From our numerical results we are able to explore a variety of phenomena, including hydrogen jetting, kinetic effects (non-Maxwellian and anisotropic distributions), plasma physics (size, persistence and role of electric fields) and transport (relative sizes of Fickean diffision, electrodiffusion and barodiffusion). As compared with the recent molecular dynamics work the kinetic model greatly extends the accessible physical domains we are able to model.

Bridging the physical scales in evolutionary biology: From protein sequence space to fitness of organisms and populations

PubMed Central

Bershtein, Shimon; Serohijos, Adrian W.R.; Shakhnovich, Eugene I.

2016-01-01

Bridging the gap between the molecular properties of proteins and organismal/population fitness is essential for understanding evolutionary processes. This task requires the integration of the several physical scales of biological organization, each defined by a distinct set of mechanisms and constraints, into a single unifying model. The molecular scale is dominated by the constraints imposed by the physico-chemical properties of proteins and their substrates, which give rise to trade-offs and epistatic (non-additive) effects of mutations. At the systems scale, biological networks modulate protein expression and can either buffer or enhance the fitness effects of mutations. The population scale is influenced by the mutational input, selection regimes, and stochastic changes affecting the size and structure of populations, which eventually determine the evolutionary fate of mutations. Here, we summarize the recent advances in theory, computer simulations, and experiments that advance our understanding of the links between various physical scales in biology. PMID:27810574

Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations.

PubMed

Bershtein, Shimon; Serohijos, Adrian Wr; Shakhnovich, Eugene I

2017-02-01

Bridging the gap between the molecular properties of proteins and organismal/population fitness is essential for understanding evolutionary processes. This task requires the integration of the several physical scales of biological organization, each defined by a distinct set of mechanisms and constraints, into a single unifying model. The molecular scale is dominated by the constraints imposed by the physico-chemical properties of proteins and their substrates, which give rise to trade-offs and epistatic (non-additive) effects of mutations. At the systems scale, biological networks modulate protein expression and can either buffer or enhance the fitness effects of mutations. The population scale is influenced by the mutational input, selection regimes, and stochastic changes affecting the size and structure of populations, which eventually determine the evolutionary fate of mutations. Here, we summarize the recent advances in theory, computer simulations, and experiments that advance our understanding of the links between various physical scales in biology. Copyright © 2016 Elsevier Ltd. All rights reserved.

Atomic and molecular far-infrared lines from high redshift galaxies

NASA Astrophysics Data System (ADS)

Vallini, L.

2015-03-01

The advent of Atacama Large Millimeter-submillimeter Array (ALMA), with its unprecedented sensitivity, makes it possible the detection of far-infrared (FIR) metal cooling and molecular lines from the first galaxies that formed after the Big Bang. These lines represent a powerful tool to shed light on the physical properties of the interstellar medium (ISM) in high-redshift sources. In what follows we show the potential of a physically motivated theoretical approach that we developed to predict the ISM properties of high redshift galaxies. The model allows to infer, as a function of the metallicity, the luminosities of various FIR lines observable with ALMA. It is based on high resolution cosmological simulations of star-forming galaxies at the end of the Epoch of Reionization (z˜eq6) , further implemented with sub-grid physics describing the cooling and the heating processes that take place in the neutral diffuse ISM. Finally we show how a different approach based on semi-analytical calculations can allow to predict the CO flux function at z>6.

Quantum Sensing for High Energy Physics

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

van Bibber, Karl; Boshier, Malcolm; Demarteau, Marcel

The Coordinating Panel for Advanced Detectors (CPAD) of the APS Division of Particles and Fields organized a first workshop on Quantum Sensing for High Energy Physics (HEP) in early December 2017 at Argonne National Laboratory. Participants from universities and national labs were drawn from the intersecting fields of Quantum Information Science (QIS), high energy physics, atomic, molecular and optical physics, condensed matter physics, nuclear physics and materials science. Quantum-enabled science and technology has seen rapid technical advances and growing national interest and investments over the last few years. The goal of the workshop was to bring the various communities togethermore » to investigate pathways to integrate the expertise of these two disciplines to accelerate the mutual advancement of scientific progress.« less

Determination of Molecular Self-Diffusion Coefficients Using Pulsed-Field-Gradient NMR: An Experiment for Undergraduate Physical Chemistry Laboratory

ERIC Educational Resources Information Center

Harmon, Jennifer; Coffman, Cierra; Villarrial, Spring; Chabolla, Steven; Heisel, Kurt A.; Krishnan, Viswanathan V.

2012-01-01

NMR spectroscopy has become one of the primary tools that chemists utilize to characterize a range of chemical species in the solution phase, from small organic molecules to medium-sized proteins. A discussion of NMR spectroscopy is an essential component of physical and biophysical chemistry lecture courses, and a number of instructional…

The Physical Properties of a Lavage Mixture of Pulmonary Surfactant, Perfluorodecaline, and Methylprednisolone (Perfactant Lavage)

DTIC Science & Technology

2014-05-09

release: distribution unlimited Purpose: To characterize the physical properties of a lavage mixture of pulmonary surfactant, perfluorocarbon and...methylprednisolone. Background: Perfluorocarbons (PFCs) are compounds derived from hydrocarbons by the substitution of hydrogen atoms with fluorine...atoms. Perfluorocarbon liquids are colorless, odorless and biologically inert. They are highly dense, due to their molecular weight. Their low

Reasoning Using Particulate Nature of Matter: An Example of a Sociochemical Norm in a University-Level Physical Chemistry Class

ERIC Educational Resources Information Center

Becker, Nicole; Rasmussen, Chris; Sweeney, George; Wawro, Megan; Towns, Marcy; Cole, Renee

2013-01-01

In college level chemistry courses, reasoning using molecular and particulate descriptions of matter becomes central to understanding physical and chemical properties. In this study, we used a qualitative approach to analyzing classroom discourse derived from Toulmin's model of argumentation in order to describe the ways in which students develop…

Simulating the Physical World

NASA Astrophysics Data System (ADS)

Berendsen, Herman J. C.

2004-06-01

The simulation of physical systems requires a simplified, hierarchical approach which models each level from the atomistic to the macroscopic scale. From quantum mechanics to fluid dynamics, this book systematically treats the broad scope of computer modeling and simulations, describing the fundamental theory behind each level of approximation. Berendsen evaluates each stage in relation to its applications giving the reader insight into the possibilities and limitations of the models. Practical guidance for applications and sample programs in Python are provided. With a strong emphasis on molecular models in chemistry and biochemistry, this book will be suitable for advanced undergraduate and graduate courses on molecular modeling and simulation within physics, biophysics, physical chemistry and materials science. It will also be a useful reference to all those working in the field. Additional resources for this title including solutions for instructors and programs are available online at www.cambridge.org/9780521835275. The first book to cover the wide range of modeling and simulations, from atomistic to the macroscopic scale, in a systematic fashion Providing a wealth of background material, it does not assume advanced knowledge and is eminently suitable for course use Contains practical examples and sample programs in Python

The relationship between the Tg depression and the speeding up of physical aging in polystyrene/gold nanocomposites

NASA Astrophysics Data System (ADS)

Boucher, Virginie M.; Cangialosi, Daniele; Alegria, Angel; Colmenero, Juan

2011-03-01

The effect of gold nanoparticles on the segmental dynamics, glass transition (Tg) and physical aging of polystyrene (PS) was studied in PS/Gold nanocomposites samples containing 5 and 15 wt.% of 60 nm spherical gold nanoparticles, surface-treated with thiolated-PS. While the segmental dynamics of PS, as assessed by broadband dielectric spectroscopy (BDS), was found to be unchanged in presence of gold nanoparticles, the calorimetric Tg of PS was shown to decrease with increasing the amount of nanoparticles in the samples. Furthermore, the physical aging of PS, monitored by measuring the enthalpy relaxation below Tg by means of DSC, was shown to speed up with increasing the nanoparticles weight fraction, i.e. the amount of PS/Gold interface in the hybrid material. Thus, the main conclusion of our work is that PS molecular mobility and out-of-equilibrium dynamics are decoupled in these nanocomposites. The significant effect of the amount of PS/Gold interface on both the physical aging rate of PS and the calorimetric Tg depression are quantitatively accounted for by a model based on the diffusion of free volume holes towards polymer interfaces, with a diffusion coefficient depending only on the molecular mobility.

The physical characteristics of human proteins in different biological functions.

PubMed

Wang, Tengjiao; Tang, Hailin

2017-01-01

The physical properties of gene products are the foundation of their biological functions. In this study, we systematically explored relationships between physical properties and biological functions. The physical properties including origin time, evolution pressure, mRNA and protein stability, molecular weight, hydrophobicity, acidity/alkaline, amino acid compositions, and chromosome location. The biological functions are defined from 4 aspects: biological process, molecular function, cellular component and cell/tissue/organ expression. We found that the proteins associated with basic material and energy metabolism process originated earlier, while the proteins associated with immune, neurological system process etc. originated later. Tissues may have a strong influence on evolution pressure. The proteins associated with energy metabolism are double-stable. Immune and peripheral cell proteins tend to be mRNA stable/protein unstable. There are very few function items with double-unstable of mRNA and protein. The proteins involved in the cell adhesion tend to consist of large proteins with high proportion of small amino acids. The proteins of organic acid transport, neurological system process and amine transport have significantly high hydrophobicity. Interestingly, the proteins involved in olfactory receptor activity tend to have high frequency of aromatic, sulfuric and hydroxyl amino acids.

The physical characteristics of human proteins in different biological functions

PubMed Central

Tang, Hailin

2017-01-01

The physical properties of gene products are the foundation of their biological functions. In this study, we systematically explored relationships between physical properties and biological functions. The physical properties including origin time, evolution pressure, mRNA and protein stability, molecular weight, hydrophobicity, acidity/alkaline, amino acid compositions, and chromosome location. The biological functions are defined from 4 aspects: biological process, molecular function, cellular component and cell/tissue/organ expression. We found that the proteins associated with basic material and energy metabolism process originated earlier, while the proteins associated with immune, neurological system process etc. originated later. Tissues may have a strong influence on evolution pressure. The proteins associated with energy metabolism are double-stable. Immune and peripheral cell proteins tend to be mRNA stable/protein unstable. There are very few function items with double-unstable of mRNA and protein. The proteins involved in the cell adhesion tend to consist of large proteins with high proportion of small amino acids. The proteins of organic acid transport, neurological system process and amine transport have significantly high hydrophobicity. Interestingly, the proteins involved in olfactory receptor activity tend to have high frequency of aromatic, sulfuric and hydroxyl amino acids. PMID:28459865

Coarse-grained, foldable, physical model of the polypeptide chain.

PubMed

Chakraborty, Promita; Zuckermann, Ronald N

2013-08-13

Although nonflexible, scaled molecular models like Pauling-Corey's and its descendants have made significant contributions in structural biology research and pedagogy, recent technical advances in 3D printing and electronics make it possible to go one step further in designing physical models of biomacromolecules: to make them conformationally dynamic. We report here the design, construction, and validation of a flexible, scaled, physical model of the polypeptide chain, which accurately reproduces the bond rotational degrees of freedom in the peptide backbone. The coarse-grained backbone model consists of repeating amide and α-carbon units, connected by mechanical bonds (corresponding to ϕ and ψ) that include realistic barriers to rotation that closely approximate those found at the molecular scale. Longer-range hydrogen-bonding interactions are also incorporated, allowing the chain to readily fold into stable secondary structures. The model is easily constructed with readily obtainable parts and promises to be a tremendous educational aid to the intuitive understanding of chain folding as the basis for macromolecular structure. Furthermore, this physical model can serve as the basis for linking tangible biomacromolecular models directly to the vast array of existing computational tools to provide an enhanced and interactive human-computer interface.

Phase Structure of Strong-Field Tunneling Wave Packets from Molecules.

PubMed

Liu, Ming-Ming; Li, Min; Wu, Chengyin; Gong, Qihuang; Staudte, André; Liu, Yunquan

2016-04-22

We study the phase structure of the tunneling wave packets from strong-field ionization of molecules and present a molecular quantum-trajectory Monte Carlo model to describe the laser-driven dynamics of photoelectron momentum distributions of molecules. Using our model, we reproduce and explain the alignment-dependent molecular frame photoelectron spectra of strong-field tunneling ionization of N_{2} reported by M. Meckel et al. [Nat. Phys. 10, 594 (2014)]. In addition to modeling the low-energy photoelectron angular distributions quantitatively, we extract the phase structure of strong-field molecular tunneling wave packets, shedding light on its physical origin. The initial phase of the tunneling wave packets at the tunnel exit depends on both the initial transverse momentum distribution and the molecular internuclear distance. We further show that the ionizing molecular orbital has a critical effect on the initial phase of the tunneling wave packets. The phase structure of the photoelectron wave packet is a key ingredient for modeling strong-field molecular photoelectron holography, high-harmonic generation, and molecular orbital imaging.

Practical quantum mechanics-based fragment methods for predicting molecular crystal properties.

PubMed

Wen, Shuhao; Nanda, Kaushik; Huang, Yuanhang; Beran, Gregory J O

2012-06-07

Significant advances in fragment-based electronic structure methods have created a real alternative to force-field and density functional techniques in condensed-phase problems such as molecular crystals. This perspective article highlights some of the important challenges in modeling molecular crystals and discusses techniques for addressing them. First, we survey recent developments in fragment-based methods for molecular crystals. Second, we use examples from our own recent research on a fragment-based QM/MM method, the hybrid many-body interaction (HMBI) model, to analyze the physical requirements for a practical and effective molecular crystal model chemistry. We demonstrate that it is possible to predict molecular crystal lattice energies to within a couple kJ mol(-1) and lattice parameters to within a few percent in small-molecule crystals. Fragment methods provide a systematically improvable approach to making predictions in the condensed phase, which is critical to making robust predictions regarding the subtle energy differences found in molecular crystals.

Lighting the dark molecular gas and a Bok globule

NASA Astrophysics Data System (ADS)

Togi, Aditya G.

Stars are the building blocks of galaxies. The gas present in galaxies is the primary fuel for star formation. Galaxy evolution depends on the amount of gas present in the interstellar medium (ISM). Stars are born mainly from molecular gas in the GMCs. Robust knowledge of the molecular hydrogen H2 gas distribution is necessary to understand star formation in galaxies. Since H2 is not readily observable in the cold interstellar medium (ISM), the molecular gas content has traditionally been inferred using indirect tracers like carbon-monoxide (CO), dust emission, gamma ray interactions, and star formation efficiency. Physical processes resulting in enhancement and reduction of these indirect tracers can result in misleading estimates of molecular gas masses. My dissertation work is based on devising a new temperature power law distribution model for H2, a direct tracer, to calculate the total molecular gas mass in galaxies. The model parameters are estimated using mid infrared (MIR) H2 rotational line fluxes obtained from IRS-Spitzer (Infrared Spectrograph-Spitzer) instrument and the model is extrapolated to a suitable lower temperature to recover the total molecular gas mass. The power law model is able to recover the dark molecular gas, undetected by CO, in galaxies at metallicity as low as one-tenth of our Milky Way value. I have applied the power law model in U/LIRGs and shocks of Stephan's Quintet to understand molecular gas properties, where shocks play an important role in exciting H2. Comparing the molecular gas content derived through our power law model can be useful in studying the application of our model in mergers. The parameters derived by our model is useful in understanding variation in molecular gas properties in shock regions of Stephan's Quintet. Low mass stars are formed in small isolated dense cores known as Bok globules. Multiple star formation events are seen in a Bok globule. In my thesis I also studied a Bok globule, B207, and determined the physical properties and future evolutionary stage of the cloud. My thesis spans studying ISM properties in galaxies from kpc to sub-pc scales. Using the power law model in the coming era of James Webb Space Telescope (JWST) with the high sensitivity MIR Instrument (MIRI) spectrograph we will be able to understand the properties of molecular gas at low and high redshifts.

REVIEWS OF TOPICAL PROBLEMS: Analytic calculations on digital computers for applications in physics and mathematics

NASA Astrophysics Data System (ADS)

Gerdt, V. P.; Tarasov, O. V.; Shirkov, Dmitrii V.

1980-01-01

The present state of analytic calculations on computers is reviewed. Several programming systems which are used for analytic calculations are discussed: SCHOONSCHIP, CLAM, REDUCE-2, SYMBAL, CAMAL, AVTO-ANALITIK, MACSYMA, etc. It is shown that these systems can be used to solve a wide range of problems in physics and mathematics. Some physical applications are discussed in celestial mechanics, the general theory of relativity, quantum field theory, plasma physics, hydrodynamics, atomic and molecular physics, and quantum chemistry. Some mathematical applications which are discussed are evaluating indefinite integrals, solving differential equations, and analyzing mathematical expressions. This review is addressed to physicists and mathematicians working in a wide range of fields.

Physics Computing '92: Proceedings of the 4th International Conference

NASA Astrophysics Data System (ADS)

de Groot, Robert A.; Nadrchal, Jaroslav

1993-04-01

The Table of Contents for the book is as follows: * Preface * INVITED PAPERS * Ab Initio Theoretical Approaches to the Structural, Electronic and Vibrational Properties of Small Clusters and Fullerenes: The State of the Art * Neural Multigrid Methods for Gauge Theories and Other Disordered Systems * Multicanonical Monte Carlo Simulations * On the Use of the Symbolic Language Maple in Physics and Chemistry: Several Examples * Nonequilibrium Phase Transitions in Catalysis and Population Models * Computer Algebra, Symmetry Analysis and Integrability of Nonlinear Evolution Equations * The Path-Integral Quantum Simulation of Hydrogen in Metals * Digital Optical Computing: A New Approach of Systolic Arrays Based on Coherence Modulation of Light and Integrated Optics Technology * Molecular Dynamics Simulations of Granular Materials * Numerical Implementation of a K.A.M. Algorithm * Quasi-Monte Carlo, Quasi-Random Numbers and Quasi-Error Estimates * What Can We Learn from QMC Simulations * Physics of Fluctuating Membranes * Plato, Apollonius, and Klein: Playing with Spheres * Steady States in Nonequilibrium Lattice Systems * CONVODE: A REDUCE Package for Differential Equations * Chaos in Coupled Rotators * Symplectic Numerical Methods for Hamiltonian Problems * Computer Simulations of Surfactant Self Assembly * High-dimensional and Very Large Cellular Automata for Immunological Shape Space * A Review of the Lattice Boltzmann Method * Electronic Structure of Solids in the Self-interaction Corrected Local-spin-density Approximation * Dedicated Computers for Lattice Gauge Theory Simulations * Physics Education: A Survey of Problems and Possible Solutions * Parallel Computing and Electronic-Structure Theory * High Precision Simulation Techniques for Lattice Field Theory * CONTRIBUTED PAPERS * Case Study of Microscale Hydrodynamics Using Molecular Dynamics and Lattice Gas Methods * Computer Modelling of the Structural and Electronic Properties of the Supported Metal Catalysis * Ordered Particle Simulations for Serial and MIMD Parallel Computers * "NOLP" -- Program Package for Laser Plasma Nonlinear Optics * Algorithms to Solve Nonlinear Least Square Problems * Distribution of Hydrogen Atoms in Pd-H Computed by Molecular Dynamics * A Ray Tracing of Optical System for Protein Crystallography Beamline at Storage Ring-SIBERIA-2 * Vibrational Properties of a Pseudobinary Linear Chain with Correlated Substitutional Disorder * Application of the Software Package Mathematica in Generalized Master Equation Method * Linelist: An Interactive Program for Analysing Beam-foil Spectra * GROMACS: A Parallel Computer for Molecular Dynamics Simulations * GROMACS Method of Virial Calculation Using a Single Sum * The Interactive Program for the Solution of the Laplace Equation with the Elimination of Singularities for Boundary Functions * Random-Number Generators: Testing Procedures and Comparison of RNG Algorithms * Micro-TOPIC: A Tokamak Plasma Impurities Code * Rotational Molecular Scattering Calculations * Orthonormal Polynomial Method for Calibrating of Cryogenic Temperature Sensors * Frame-based System Representing Basis of Physics * The Role of Massively Data-parallel Computers in Large Scale Molecular Dynamics Simulations * Short-range Molecular Dynamics on a Network of Processors and Workstations * An Algorithm for Higher-order Perturbation Theory in Radiative Transfer Computations * Hydrostochastics: The Master Equation Formulation of Fluid Dynamics * HPP Lattice Gas on Transputers and Networked Workstations * Study on the Hysteresis Cycle Simulation Using Modeling with Different Functions on Intervals * Refined Pruning Techniques for Feed-forward Neural Networks * Random Walk Simulation of the Motion of Transient Charges in Photoconductors * The Optical Hysteresis in Hydrogenated Amorphous Silicon * Diffusion Monte Carlo Analysis of Modern Interatomic Potentials for He * A Parallel Strategy for Molecular Dynamics Simulations of Polar Liquids on Transputer Arrays * Distribution of Ions Reflected on Rough Surfaces * The Study of Step Density Distribution During Molecular Beam Epitaxy Growth: Monte Carlo Computer Simulation * Towards a Formal Approach to the Construction of Large-scale Scientific Applications Software * Correlated Random Walk and Discrete Modelling of Propagation through Inhomogeneous Media * Teaching Plasma Physics Simulation * A Theoretical Determination of the Au-Ni Phase Diagram * Boson and Fermion Kinetics in One-dimensional Lattices * Computational Physics Course on the Technical University * Symbolic Computations in Simulation Code Development and Femtosecond-pulse Laser-plasma Interaction Studies * Computer Algebra and Integrated Computing Systems in Education of Physical Sciences * Coordinated System of Programs for Undergraduate Physics Instruction * Program Package MIRIAM and Atomic Physics of Extreme Systems * High Energy Physics Simulation on the T_Node * The Chapman-Kolmogorov Equation as Representation of Huygens' Principle and the Monolithic Self-consistent Numerical Modelling of Lasers * Authoring System for Simulation Developments * Molecular Dynamics Study of Ion Charge Effects in the Structure of Ionic Crystals * A Computational Physics Introductory Course * Computer Calculation of Substrate Temperature Field in MBE System * Multimagnetical Simulation of the Ising Model in Two and Three Dimensions * Failure of the CTRW Treatment of the Quasicoherent Excitation Transfer * Implementation of a Parallel Conjugate Gradient Method for Simulation of Elastic Light Scattering * Algorithms for Study of Thin Film Growth * Algorithms and Programs for Physics Teaching in Romanian Technical Universities * Multicanonical Simulation of 1st order Transitions: Interface Tension of the 2D 7-State Potts Model * Two Numerical Methods for the Calculation of Periodic Orbits in Hamiltonian Systems * Chaotic Behavior in a Probabilistic Cellular Automata? * Wave Optics Computing by a Networked-based Vector Wave Automaton * Tensor Manipulation Package in REDUCE * Propagation of Electromagnetic Pulses in Stratified Media * The Simple Molecular Dynamics Model for the Study of Thermalization of the Hot Nucleon Gas * Electron Spin Polarization in PdCo Alloys Calculated by KKR-CPA-LSD Method * Simulation Studies of Microscopic Droplet Spreading * A Vectorizable Algorithm for the Multicolor Successive Overrelaxation Method * Tetragonality of the CuAu I Lattice and Its Relation to Electronic Specific Heat and Spin Susceptibility * Computer Simulation of the Formation of Metallic Aggregates Produced by Chemical Reactions in Aqueous Solution * Scaling in Growth Models with Diffusion: A Monte Carlo Study * The Nucleus as the Mesoscopic System * Neural Network Computation as Dynamic System Simulation * First-principles Theory of Surface Segregation in Binary Alloys * Data Smooth Approximation Algorithm for Estimating the Temperature Dependence of the Ice Nucleation Rate * Genetic Algorithms in Optical Design * Application of 2D-FFT in the Study of Molecular Exchange Processes by NMR * Advanced Mobility Model for Electron Transport in P-Si Inversion Layers * Computer Simulation for Film Surfaces and its Fractal Dimension * Parallel Computation Techniques and the Structure of Catalyst Surfaces * Educational SW to Teach Digital Electronics and the Corresponding Text Book * Primitive Trinomials (Mod 2) Whose Degree is a Mersenne Exponent * Stochastic Modelisation and Parallel Computing * Remarks on the Hybrid Monte Carlo Algorithm for the ∫4 Model * An Experimental Computer Assisted Workbench for Physics Teaching * A Fully Implicit Code to Model Tokamak Plasma Edge Transport * EXPFIT: An Interactive Program for Automatic Beam-foil Decay Curve Analysis * Mapping Technique for Solving General, 1-D Hamiltonian Systems * Freeway Traffic, Cellular Automata, and Some (Self-Organizing) Criticality * Photonuclear Yield Analysis by Dynamic Programming * Incremental Representation of the Simply Connected Planar Curves * Self-convergence in Monte Carlo Methods * Adaptive Mesh Technique for Shock Wave Propagation * Simulation of Supersonic Coronal Streams and Their Interaction with the Solar Wind * The Nature of Chaos in Two Systems of Ordinary Nonlinear Differential Equations * Considerations of a Window-shopper * Interpretation of Data Obtained by RTP 4-Channel Pulsed Radar Reflectometer Using a Multi Layer Perceptron * Statistics of Lattice Bosons for Finite Systems * Fractal Based Image Compression with Affine Transformations * Algorithmic Studies on Simulation Codes for Heavy-ion Reactions * An Energy-Wise Computer Simulation of DNA-Ion-Water Interactions Explains the Abnormal Structure of Poly[d(A)]:Poly[d(T)] * Computer Simulation Study of Kosterlitz-Thouless-Like Transitions * Problem-oriented Software Package GUN-EBT for Computer Simulation of Beam Formation and Transport in Technological Electron-Optical Systems * Parallelization of a Boundary Value Solver and its Application in Nonlinear Dynamics * The Symbolic Classification of Real Four-dimensional Lie Algebras * Short, Singular Pulses Generation by a Dye Laser at Two Wavelengths Simultaneously * Quantum Monte Carlo Simulations of the Apex-Oxygen-Model * Approximation Procedures for the Axial Symmetric Static Einstein-Maxwell-Higgs Theory * Crystallization on a Sphere: Parallel Simulation on a Transputer Network * FAMULUS: A Software Product (also) for Physics Education * MathCAD vs. FAMULUS -- A Brief Comparison * First-principles Dynamics Used to Study Dissociative Chemisorption * A Computer Controlled System for Crystal Growth from Melt * A Time Resolved Spectroscopic Method for Short Pulsed Particle Emission * Green's Function Computation in Radiative Transfer Theory * Random Search Optimization Technique for One-criteria and Multi-criteria Problems * Hartley Transform Applications to Thermal Drift Elimination in Scanning Tunneling Microscopy * Algorithms of Measuring, Processing and Interpretation of Experimental Data Obtained with Scanning Tunneling Microscope * Time-dependent Atom-surface Interactions * Local and Global Minima on Molecular Potential Energy Surfaces: An Example of N3 Radical * Computation of Bifurcation Surfaces * Symbolic Computations in Quantum Mechanics: Energies in Next-to-solvable Systems * A Tool for RTP Reactor and Lamp Field Design * Modelling of Particle Spectra for the Analysis of Solid State Surface * List of Participants

Molecular dynamics simulations through GPU video games technologies

PubMed Central

Loukatou, Styliani; Papageorgiou, Louis; Fakourelis, Paraskevas; Filntisi, Arianna; Polychronidou, Eleftheria; Bassis, Ioannis; Megalooikonomou, Vasileios; Makałowski, Wojciech; Vlachakis, Dimitrios; Kossida, Sophia

2016-01-01

Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations. PMID:27525251

Factors determining electrostatic fields in molecular dynamics simulations of the Ras/effector interface.

PubMed

Ensign, Daniel L; Webb, Lauren J

2011-12-01

Using molecular dynamics simulations, we explore geometric and physical factors contributing to calculated electrostatic fields at the binding surface of the GTPase Ras with a spectroscopically labeled variant of a downstream effector, the Ras-binding domain of Ral guanine nucleotide dissociation stimulator (RalGDS). A related system (differing by mutation of one amino acid) has been studied in our group using vibrational Stark effect spectroscopy, a technique sensitive to electrostatic fields. Electrostatic fields were computed using the AMBER 2003 force field and averaged over snapshots from molecular dynamics simulation. We investigate geometric factors by exploring how the orientation of the spectroscopic probe changes on Ras-effector binding. In addition, we explore the physical origin of electrostatic fields at our spectroscopic probe by comparing contributions to the field from discrete components of the system, such as explicit solvent, residues on the Ras surface, and residues on the RalGDS surface. These models support our experimental hypothesis that vibrational Stark shifts are caused by Ras binding to its effector and not the structural rearrangements of the effector surface or probe reorientation on Ras-effector binding, for at least some of our experimental probes. These calculations provide physical insight into the origin, magnitude, and importance of electrostatic fields in protein-protein interactions and suggest new experiments to probe the field's role in protein docking. Copyright © 2011 Wiley-Liss, Inc.

ngVLA Key Science Goal 2: Probing the Initial Conditions for Planetary Systems and Life with Astrochemistry

NASA Astrophysics Data System (ADS)

McGuire, Brett; ngVLA Science Working Group 1

2018-01-01

One of the most challenging aspects in understanding the origin and evolution of planets and planetary systems is tracing the influence of chemistry on the physical evolution of a system from a molecular cloud to a solar system. Existing facilities have already shown the stunning degree of molecular complexity present in these systems. The unique combination of sensitivity and spatial resolution offered by the ngVLA will permit the observation of both highly complex and very low-abundance chemical species that are exquisitely sensitive to the physical conditions and evolutionary history of their sources, which are out of reach of current observatories. In turn, by understanding the chemical evolution of these complex molecules, unprecedentedly detailed astrophysical insight can be gleaned from these astrochemical observations.This poster will overview a number of key science goals in astrochemistry which will be enabled by the ngVLA, including:1) imaging of the deepest, densest regions in protoplanetary disks and unveiling the physical history through isotopic ratios2) probing the ammonia snow line in these disks, thought to be the only viable tracer of the water snowline3) observations of the molecular content of giant planet atmospheres4) detections of new, complex molecules, potentially including the simplest amino acids and sugars5) tracing the origin of chiral excess in star-forming regions

The effects of polymer carrier, hot melt extrusion process and downstream processing parameters on the moisture sorption properties of amorphous solid dispersions.

PubMed

Feng, Xin; Vo, Anh; Patil, Hemlata; Tiwari, Roshan V; Alshetaili, Abdullah S; Pimparade, Manjeet B; Repka, Michael A

2016-05-01

The aim of this study was to evaluate the effect of polymer carrier, hot melt extrusion and downstream processing parameters on the water uptake properties of amorphous solid dispersions. Three polymers and a model drug were used to prepare amorphous solid dispersions utilizing the hot melt extrusion technology. The sorption-desorption isotherms of solid dispersions and their physical mixtures were measured by the dynamic vapour sorption system, and the effects of polymer hydrophobicity, hygroscopicity, molecular weight and the hot melt extrusion process were investigated. Fourier transform infrared (FTIR) imaging was performed to understand the phase separation driven by the moisture. Solid dispersions with polymeric carriers with lower hydrophilicity, hygroscopicity and higher molecular weight could sorb less moisture under the high relative humidity (RH) conditions. The water uptake ability of polymer-drug solid dispersion systems were decreased compared with the physical mixture after hot melt extrusion, which might be due to the decreased surface area and porosity. The FTIR imaging indicated that the homogeneity of the drug molecularly dispersed within the polymer matrix was changed after exposure to high RH. Understanding the effect of formulation and processing on the moisture sorption properties of solid dispersions is essential for the development of drug products with desired physical and chemical stability. © 2015 Royal Pharmaceutical Society.

Mechanics of neurulation: From classical to current perspectives on the physical mechanics that shape, fold, and form the neural tube.

PubMed

Vijayraghavan, Deepthi S; Davidson, Lance A

2017-01-30

Neural tube defects arise from mechanical failures in the process of neurulation. At the most fundamental level, formation of the neural tube relies on coordinated, complex tissue movements that mechanically transform the flat neural epithelium into a lumenized epithelial tube (Davidson, 2012). The nature of this mechanical transformation has mystified embryologists, geneticists, and clinicians for more than 100 years. Early embryologists pondered the physical mechanisms that guide this transformation. Detailed observations of cell and tissue movements as well as experimental embryological manipulations allowed researchers to generate and test elementary hypotheses of the intrinsic and extrinsic forces acting on the neural tissue. Current research has turned toward understanding the molecular mechanisms underlying neurulation. Genetic and molecular perturbation have identified a multitude of subcellular components that correlate with cell behaviors and tissue movements during neural tube formation. In this review, we focus on methods and conceptual frameworks that have been applied to the study of amphibian neurulation that can be used to determine how molecular and physical mechanisms are integrated and responsible for neurulation. We will describe how qualitative descriptions and quantitative measurements of strain, force generation, and tissue material properties as well as simulations can be used to understand how embryos use morphogenetic programs to drive neurulation. Birth Defects Research 109:153-168, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Global Analysis of Gene Expression Profiles in Physic Nut (Jatropha curcas L.) Seedlings Exposed to Salt Stress

PubMed Central

Wu, Pingzhi; Chen, Yaping; Li, Meiru; Jiang, Huawu; Wu, Guojiang

2014-01-01

Background Salt stress interferes with plant growth and production. Plants have evolved a series of molecular and morphological adaptations to cope with this abiotic stress, and overexpression of salt response genes reportedly enhances the productivity of various crops. However, little is known about the salt responsive genes in the energy plant physic nut (Jatropha curcas L.). Thus, excavate salt responsive genes in this plant are informative in uncovering the molecular mechanisms for the salt response in physic nut. Methodology/Principal Findings We applied next-generation Illumina sequencing technology to analyze global gene expression profiles of physic nut plants (roots and leaves) 2 hours, 2 days and 7 days after the onset of salt stress. A total of 1,504 and 1,115 genes were significantly up and down-regulated in roots and leaves, respectively, under salt stress condition. Gene ontology (GO) analysis of physiological process revealed that, in the physic nut, many “biological processes” were affected by salt stress, particular those categories belong to “metabolic process”, such as “primary metabolism process”, “cellular metabolism process” and “macromolecule metabolism process”. The gene expression profiles indicated that the associated genes were responsible for ABA and ethylene signaling, osmotic regulation, the reactive oxygen species scavenging system and the cell structure in physic nut. Conclusions/Significance The major regulated genes detected in this transcriptomic data were related to trehalose synthesis and cell wall structure modification in roots, while related to raffinose synthesis and reactive oxygen scavenger in leaves. The current study shows a comprehensive gene expression profile of physic nut under salt stress. The differential expression genes detected in this study allows the underling the salt responsive mechanism in physic nut with the aim of improving its salt resistance in the future. PMID:24837971

Global analysis of gene expression profiles in physic nut (Jatropha curcas L.) seedlings exposed to salt stress.

PubMed

Zhang, Lin; Zhang, Chao; Wu, Pingzhi; Chen, Yaping; Li, Meiru; Jiang, Huawu; Wu, Guojiang

2014-01-01

Salt stress interferes with plant growth and production. Plants have evolved a series of molecular and morphological adaptations to cope with this abiotic stress, and overexpression of salt response genes reportedly enhances the productivity of various crops. However, little is known about the salt responsive genes in the energy plant physic nut (Jatropha curcas L.). Thus, excavate salt responsive genes in this plant are informative in uncovering the molecular mechanisms for the salt response in physic nut. We applied next-generation Illumina sequencing technology to analyze global gene expression profiles of physic nut plants (roots and leaves) 2 hours, 2 days and 7 days after the onset of salt stress. A total of 1,504 and 1,115 genes were significantly up and down-regulated in roots and leaves, respectively, under salt stress condition. Gene ontology (GO) analysis of physiological process revealed that, in the physic nut, many "biological processes" were affected by salt stress, particular those categories belong to "metabolic process", such as "primary metabolism process", "cellular metabolism process" and "macromolecule metabolism process". The gene expression profiles indicated that the associated genes were responsible for ABA and ethylene signaling, osmotic regulation, the reactive oxygen species scavenging system and the cell structure in physic nut. The major regulated genes detected in this transcriptomic data were related to trehalose synthesis and cell wall structure modification in roots, while related to raffinose synthesis and reactive oxygen scavenger in leaves. The current study shows a comprehensive gene expression profile of physic nut under salt stress. The differential expression genes detected in this study allows the underling the salt responsive mechanism in physic nut with the aim of improving its salt resistance in the future.

Possible Circuit Architectures for Molecular Nanoelectronics

NASA Astrophysics Data System (ADS)

Likharev, Konstantin

2003-03-01

Chemically-directed self-assembly of molecular devices is apparently the only feasible way to continue the fast progress of microelectronics after its Moore-Laws-based development runs into the wall of physical and economic limitations [1]. The architectures of VLSI circuits using such devices should be substantially fault-tolerant and accommodate other their features including low transconductance. The most significant feature of all promising suggested architectures is the hybridization of three technologies: advanced CMOS, simple nanowire arrays, and molecular devices self-assembling on these wires. Molecular memory arrays may have a simple structure, and their simple prototypes have already been implemented experimentally [2]. In contrast, the logic circuit development is just starting. I will describe a family of neuromorphic networks based on so-called CrossNet arrays [3] that look promising for advanced information processing, starting from fast image recognition and beyond. This architecture may combine very high density (above 10^12 functions per cm^2) and relatively high speed (100-ns-scale latency of cell-to-cell communications) at acceptable power consumption. In future, these features may allow to put an artificial analog of the human cerebral cortex, capable of processing information and (hopefully) self-evolution at 4 to 5 orders of magnitude faster than its biological prototype, on a 20x20 cm^2 silicon wafer. [1] K. Likharev, "Electronics Below 20-nm", see http://rsfq1.physics.sunysb.edu/ likharev/nano/ForMorkoc.pdf. [2] See, e.g, http://nanotechweb.org/articles/news/1/9/8/1. [3] O. Turel and K. Likharev, Int. J. of Circuit Theory and Applications 31, No.1 (2003); see http://rsfq1.physics.sunysb.edu/ likharev/nano/Preprint070102.pdf.

Modulation of circular current and associated magnetic field in a molecular junction: A new approach

NASA Astrophysics Data System (ADS)

Patra, Moumita; Maiti, Santanu K.

2017-03-01

A new proposal is given to control local magnetic field in a molecular junction. In presence of finite bias a net circular current is established in the molecular ring which induces a magnetic field at its centre. Allowing a direct coupling between two electrodes, due to their close proximity, and changing its strength we can regulate circular current as well as magnetic field for a wide range, without disturbing any other physical parameters. We strongly believe that our proposal is quite robust compared to existing approaches of controlling local magnetic field and can be verified experimentally.

The Basic Principles of FDG-PET/CT Imaging.

PubMed

Basu, Sandip; Hess, Søren; Nielsen Braad, Poul-Erik; Olsen, Birgitte Brinkmann; Inglev, Signe; Høilund-Carlsen, Poul Flemming

2014-10-01

Positron emission tomography (PET) imaging with 2-[(18)F]fluoro-2-deoxy-D-glucose (FDG) forms the basis of molecular imaging. FDG-PET imaging is a multidisciplinary undertaking that requires close interdisciplinary collaboration in a broad team comprising physicians, technologists, secretaries, radio-chemists, hospital physicists, molecular biologists, engineers, and cyclotron technicians. The aim of this review is to provide a brief overview of important basic issues and considerations pivotal to successful patient examinations, including basic physics, instrumentation, radiochemistry, molecular and cell biology, patient preparation, normal distribution of tracer, and potential interpretive pitfalls. Copyright © 2014 Elsevier Inc. All rights reserved.

Seeing the Forest Through the Trees: The Distribution and Properties of Dense Molecular Gas in the Milky Way Galaxy

NASA Astrophysics Data System (ADS)

Ellsworth-Bowers, Timothy P.

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

Properties of the Excited States of Molecular Ions.

DTIC Science & Technology

1981-04-13

FIg. 1). techniques have beest applied to the study of quartet states of Oi. The four potential curves most relevant Guyon et al., using a synchrotron...8217 a’ a a C ’U ~ ~ ~ ~ ~ ~ ~ 2 2,~ C a ’I C~- C ’ 𔃺 𔃺 𔃺 ’ ’ C- ~ C-E-38- ’- u A() A09a 265 SRI INTERNATIONAL 14FNLO PARK CA MOLECULAR PHYSICS LAB F

Beyond the Alphabet Soup: Molecular Properties of Aerosol Components Influence Optics. (Invited)

NASA Astrophysics Data System (ADS)

Thompson, J. E.

2013-12-01

Components within atmospheric aerosols exhibit almost every imaginable model of chemical bonding and physical diversity. The materials run the spectrum from crystalline to amorphous, covalent to ionic, and have varying viscosities, phase, and hygroscopicity. This seminar will focus on the molecular properties of materials that influence the optical behavior of aerosols. Special focus will be placed on the polarizability of materials, hygroscopic growth, and particle phase.

Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect

NASA Astrophysics Data System (ADS)

Nakagawa, Satoshi; Kurniawan, Isman; Kodama, Koichi; Arwansyah, Muhammad Saleh; Kawaguchi, Kazutomo; Nagao, Hidemi

2018-03-01

We present a simple coarse-grained model with the molecular crowding effect in solvent to investigate the structure and dynamics of protein complexes including association and/or dissociation processes and investigate some physical properties such as the structure and the reaction rate from the viewpoint of the hydrophobic intermolecular interactions of protein complex. In the present coarse-grained model, a function depending upon the density of hydrophobic amino acid residues in a binding area of the complex is introduced, and the function involves the molecular crowding effect for the intermolecular interactions of hydrophobic amino acid residues between proteins. We propose a hydrophobic intermolecular potential energy between proteins by using the density-dependent function. The present coarse-grained model is applied to the complex of cytochrome f and plastocyanin by using the Langevin dynamics simulation to investigate some physical properties such as the complex structure, the electron transfer reaction rate constant from plastocyanin to cytochrome f and so on. We find that for proceeding the electron transfer reaction, the distance between metals in their active sites is necessary within about 18 Å. We discuss some typical complex structures formed in the present simulation in relation to the molecular crowding effect on hydrophobic interactions.

REVIEW ARTICLE: The physics of biological molecular motors

NASA Astrophysics Data System (ADS)

Thomas, N.; Thornhill, R. A.

1998-02-01

Molecular motors are the fundamental agents of movement in living organisms. A prime example is the actomyosin motor that powers muscle contraction. We illustrate the remarkable physics of this motor using a simplified three-state model, in which a myosin cross-bridge attaches to an actin filament, tilts over and then detaches. This `cross-bridge cycle', driven by ATP hydrolysis, is similar to a thermodynamic cycle, except that the molecular system is stochastic. Random transitions in the cycle therefore produce tension fluctuations, which have recently been observed in single-molecule experiments. Furthermore, since the rate constants for attachment and tilting depend on the elastic energy in the cross-bridge spring, the molecular motor is a highly nonlinear mechanical system. A bias tension `stretch activates' the motor, and it then develops the remarkable property of `negative viscosity', which allows it to perform as a self-sustained mechanical oscillator. However, when a series of attachment sites is available, the motor operates instead as a ratchet, pulling the actin filament rapidly forwards against a light load, whilst a heavy load pulls the filament only very slowly in the opposite direction. Similar ideas may apply to the dynein-tubulin motor that powers cilia and flagella and the kinesin-tubulin motor used in intracellular transport.

Multiple-time-scale motion in molecularly linked nanoparticle arrays.

PubMed

George, Christopher; Szleifer, Igal; Ratner, Mark

2013-01-22

We explore the transport of electrons between electrodes that encase a two-dimensional array of metallic quantum dots linked by molecular bridges (such as α,ω alkaline dithiols). Because the molecules can move at finite temperatures, the entire transport structure comprising the quantum dots and the molecules is in dynamical motion while the charge is being transported. There are then several physical processes (physical excursions of molecules and quantum dots, electronic migration, ordinary vibrations), all of which influence electronic transport. Each can occur on a different time scale. It is therefore not appropriate to use standard approaches to this sort of electron transfer problem. Instead, we present a treatment in which three different theoretical approaches-kinetic Monte Carlo, classical molecular dynamics, and quantum transport-are all employed. In certain limits, some of the dynamical effects are unimportant. But in general, the transport seems to follow a sort of dynamic bond percolation picture, an approach originally introduced as formal models and later applied to polymer electrolytes. Different rate-determining steps occur in different limits. This approach offers a powerful scheme for dealing with multiple time scale transport problems, as will exist in many situations with several pathways through molecular arrays or even individual molecules that are dynamically disordered.

The effect of water plasticization on the molecular mobility and crystallization tendency of amorphous disaccharides.

PubMed

Heljo, Ville Petteri; Nordberg, Antti; Tenho, Mikko; Virtanen, Tommi; Jouppila, Kirsi; Salonen, Jarno; Maunu, Sirkka Liisa; Juppo, Anne Mari

2012-10-01

To study how water plasticization affects the molecular mobility and crystallization tendency of freeze-dried trehalose, sucrose, melibiose and cellobiose. Freeze-dried disaccharides were subjected to different relative humidity atmospheres and their physical stabilities were evaluated. Lyophilizate water sorption tendencies and glass transition temperatures were modeled using Brunauer-Emmett-Teller (BET) and Gordon-Taylor (GT) equations, respectively. Sucrose and cellobiose crystallization tendencies were compared by using the concept of reduced crystallization temperature (RCT), and the molecular mobilities of trehalose and melibiose were compared by measuring their T(1)H relaxation time constants. Based on the BET and GT models, water sorption tendency and the resulting plasticizing effect were different in sucrose when compared to the other disaccharides. Trehalose and melibiose exhibited generally slower crystallization rates when compared to sucrose and cellobiose. Amorphous melibiose was shown to be particularly stable within the studied water content range, which may have partly been caused by its relatively slow molecular mobility. Slow amorphous-to-crystalline transition rate is known to be important for lyoprotecting excipients when formulating a robust drug product. The physical stabilities of amorphous trehalose and melibiose even with relatively high water contents might make their use advantageous in this respect compared to sucrose and cellobiose.

Physical stability of the amorphous anticholesterol agent (ezetimibe): the role of molecular mobility.

PubMed

Knapik, J; Wojnarowska, Z; Grzybowska, K; Hawelek, L; Sawicki, W; Wlodarski, K; Markowski, J; Paluch, M

2014-11-03

The purpose of this paper is to examine the role of molecular mobility in the recrystallization process from the amorphous state of the anticholesterol drug ezetimibe. Both the molecular dynamics and crystallization kinetics have been studied using various experimental techniques, such as broadband dielectric spectroscopy (BDS), differential scanning calorimetry (DSC), and X-ray diffraction (XRD). Our investigations have shown that ezetimibe easily recrystallizes from the disordered state, both below and above its glass transition temperature (Tg = 336 K). Moreover, we found that an only slightly elevated pressure (5 MPa) significantly accelerates the recrystallization process at T > Tg. We predict that the structural relaxation time of amorphous ezetimibe at 293 K (storage temperature) and ambient pressure is only 22 days. This result corresponds to the characteristic time, determined from XRD measurements, for amorphous ezetimibe to recrystallize during storage at Troom = 298 K. It leads to the conclusion that the molecular mobility reflected in structural relaxation of ezetimibe is mainly responsible for devitrification of this drug. Finally, we determined a relatively easy way to improve the physical stability of the drug by preparing a binary amorphous ezetimibe-Soluplus mixture. Ezetimibe in an amorphous mixture with 20 wt % Soluplus has a much better (over six times) solubility than the pure crystalline material.

Generalized Green's function molecular dynamics for canonical ensemble simulations

NASA Astrophysics Data System (ADS)

Coluci, V. R.; Dantas, S. O.; Tewary, V. K.

2018-05-01

The need of small integration time steps (˜1 fs) in conventional molecular dynamics simulations is an important issue that inhibits the study of physical, chemical, and biological systems in real timescales. Additionally, to simulate those systems in contact with a thermal bath, thermostating techniques are usually applied. In this work, we generalize the Green's function molecular dynamics technique to allow simulations within the canonical ensemble. By applying this technique to one-dimensional systems, we were able to correctly describe important thermodynamic properties such as the temperature fluctuations, the temperature distribution, and the velocity autocorrelation function. We show that the proposed technique also allows the use of time steps one order of magnitude larger than those typically used in conventional molecular dynamics simulations. We expect that this technique can be used in long-timescale molecular dynamics simulations.

The 2011 Dynamics of Molecular Collisions Conference

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

Nesbitt, David J.

The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical &more » experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor Yuan T. Lee & Professor George Schatz. Professor Lee’s research has been based on the development & use of advanced chemical kinetics & molecular beams to investigate & manipulate the behavior of fundamental chemical reactions. Lee’s work has been recognized by many awards, including the Nobel Prize for Chemistry in 1986, as well as Sloan Fellow, Dreyfus Scholar, Fellowship in the American Academy of Arts & Sciences, Fellowship in the American Physical Society, Guggenheim Fellow, Member National Academy of Sciences, Member Academia Sinica, E.O. Lawrence Award, Miller Professor, Berkeley, Fairchild Distinguished Scholar, Harrison Howe Award, Peter Debye Award, & the National Medal of Science. Lee also has served as the President of the Academia Sinica in Taiwan (ROC). Professor Schatz’s research group is interested in using theory & computation to describe physical phenomena in a broad range of applications relevant to chemistry, physics, biology & engineering. Among the types of applications that we interested are: optical properties of nanoparticles & nanoparticle assemblies; using theory to model polymer properties; DNA structure, thermodynamics & dynamics; modeling self assembly & nanopatterning; & gas phase reaction dynamics. Among his many awards & distinctions have been appointment as an Alfred P. Sloan Research Fellow, Camille & Henry Dreyfus Teacher-Scholar, the Fresenius Award, Fellow of the American Physical Society, the Max Planck Research Award, Fellowship in the American Association for the Advancement of Science, & election to the International Academy of Quantum Molecular Sciences & the American Academy of Arts & Sciences. Dr Schatz is also lauded for his highly successful work as Editor for the Journal of Physical Chemistry. We requested $10,000 from DOE in support of this meeting. The money was distributed widely among the student & post doctoral fellows & some used to attract the very best scientists in the field. The organizers were committed to encouraging women & minorities as well as encourage the field of Chemical Physics in scientifically developing countries. For example, it has been a tradition of the DMC meeting to offer of order 40 scholarships for students & postdocs to defray registration & travel costs. The benefits of increased graduate student & post doctoral attendance at the meeting cannot be over emphasized. First, these young scientists have the opportunity to present their work by means of the poster session & to a gathering of experts in their field. Secondly the limited size of the meeting allows student & young postdocs to meet & interact directly with experts in their area, to network with their peers at other institutions & become aware of career opportunities. Graduate students & post doctoral fellows are the life blood of our field. Support of their attendance at this & other similar meetings will ensure a continued flow of young talent into many areas of research represented by the DMC meeting & important to DOE.« less

Symmetry Beyond Perturbation Theory: Floppy Molecules and Rotation-Vibration States

NASA Astrophysics Data System (ADS)

Schmiedt, Hanno; Schlemmer, Stephan; Jensen, Per

2015-06-01

In the customary approach to the theoretical description of the nuclear motion in molecules, the molecule is seen as a near-static structure rotating in space. Vibrational motion causing small structural deformations induces a perturbative treatment of the rotation-vibration interaction, which fails in fluxional molecules, where all vibrational motions are large compared to the linear extension of the molecule. An example is protonated methane (CH_5^+). For this molecule, customary theory fails to simulate reliably even the low-energy spectrum. Within the traditional view of rotation and vibration being near-separable, rotational and vibrational wavefunctions can be symmetry classified separately in the molecular symmetry (MS) group. In the present contribution we discuss a fundamental group theoretical approach to the problem of determining the symmetries of molecular rotation-vibration states. We will show that all MS groups discussed so far are subgroups of the special orthogonal group in three dimensions SO(3) This leads to a group theoretical foundation of the technique of equivalent rotations. The MS group of protonated methane (G240) represents, to the best of our knowledge, the first example of an MS group which is not a subgroup of SO(3) (nor of O(3) nor of SU(2)). Because of this, a separate symmetry classification of vibrational and rotational wavefunctions becomes impossible in this MS group, consistent with the fact that a decoupling of vibrational and rotational motion is impossible. We want to discuss the consequences of this. In conclusion, we show that the prototypical floppy molecule CH_5^+ represents a new class of molecules, where usual group theoretical methods for determining selection rules and spectral assignments fail so that new methods have to be developed. P. Kumar and D. Marx, Physical Chemistry Chemical Physics 8, 573 (2006) Z. Jin, B. J. Braams, and J. M. Bowman, The Journal of Physical Chemistry A 110, 1569 (2006) A. S. Petit, J. E. Ford, and A. B. McCoy, The Journal of Physical Chemistry A 118, 7206 (2014). P.R. Bunker and P. Jensen, Molecular Symmetry and Spectroscopy (NRC Research Press, Ottawa, Canada, 1988 Being precise, we must include O(3) and SU(2), but our theory can be easily extended to these two groups. H. Longuet-Higgins, Molecular Physics 6, 445 (1963).

Observations of Pre-Stellar Cores

NASA Astrophysics Data System (ADS)

Tafalla, M.

2005-08-01

Our understanding of the physical and chemical structure of pre-stellar cores, the simplest star-forming sites, has significantly improved since the last IAU Symposium on Astrochemistry (South Korea, 1999). Research done over these years has revealed that major molecular species like CO and CS systematically deplete onto dust grains in the interior of pre-stellar cores, while species like N2H+ and NH3 survive in the gas phase and can usually be detected toward the core centers. Such a selective behavior of molecular species gives rise to a differentiated (onion-like) chemical composition, and manifests itself in molecular maps as a dichotomy between centrally peaked and ring-shaped distributions. From the point of view of star-formation studies, the identification of molecular inhomogeneities in cores helps to resolve past discrepancies between observations made using different tracers, and brings the possibility of self-consistent modelling of the core internal structure. Here I present recent work on determining the physical and chemical structure of two pre-stellar cores, L1498 and L1517B, using observations in a large number of molecules and Monte Carlo radiative transfer analysis. These two cores are typical examples of the pre-stellar core population, and their chemical composition is characterized by the presence of large `freeze out holes' in most molecular species. In contrast with these chemically processed objects, a new population of chemically young cores has begun to emerge. The characteristics of its most extreme representative, L1521E, are briefly reviewed.

FOREST unbiased Galactic plane imaging survey with the Nobeyama 45 m telescope (FUGIN). I. Project overview and initial results

NASA Astrophysics Data System (ADS)

Umemoto, Tomofumi; Minamidani, Tetsuhiro; Kuno, Nario; Fujita, Shinji; Matsuo, Mitsuhiro; Nishimura, Atsushi; Torii, Kazufumi; Tosaki, Tomoka; Kohno, Mikito; Kuriki, Mika; Tsuda, Yuya; Hirota, Akihiko; Ohashi, Satoshi; Yamagishi, Mitsuyoshi; Handa, Toshihiro; Nakanishi, Hiroyuki; Omodaka, Toshihiro; Koide, Nagito; Matsumoto, Naoko; Onishi, Toshikazu; Tokuda, Kazuki; Seta, Masumichi; Kobayashi, Yukinori; Tachihara, Kengo; Sano, Hidetoshi; Hattori, Yusuke; Onodera, Sachiko; Oasa, Yumiko; Kamegai, Kazuhisa; Tsuboi, Masato; Sofue, Yoshiaki; Higuchi, Aya E.; Chibueze, James O.; Mizuno, Norikazu; Honma, Mareki; Muller, Erik; Inoue, Tsuyoshi; Morokuma-Matsui, Kana; Shinnaga, Hiroko; Ozawa, Takeaki; Takahashi, Ryo; Yoshiike, Satoshi; Costes, Jean; Kuwahara, Sho

2017-10-01

The FUGIN project is one of legacy projects using a new multi-beam FOREST (four-beam receiver system on the 45 m telescope). This project aims to simultaneously investigate the distribution, kinematics, and physical properties of both diffuse and dense molecular gases in the Galaxy by observing 12CO, 13CO, and C18O J = 1-0 lines simultaneously. Mapping regions are parts of the first quadrant (10° ≤ l ≤ 50°, |b| ≤ 1°) and the third quadrant (198° ≤ l ≤ 236°, |b| ≤ 1°) of the Galaxy, where spiral arms, bar structure, and the molecular gas ring are included. This survey achieves the highest angular resolution to date (˜20″) for the Galactic plane survey in the CO J = 1-0 lines, which makes it possible to find dense clumps located farther away than the previous surveys. FUGIN will provide us an invaluable dataset for investigating the physics of the Galactic interstellar medium (ISM), particularly the evolution of interstellar gas covering galactic-scale structures to the internal structures of giant molecular clouds, such as small filaments/clumps/cores. We present an overview of the FUGIN project, the observation plan and initial results. These results reveal wide-field and detailed structures of molecular clouds, such as entangled filaments that have not been obvious in previous surveys, and large-scale kinematics of molecular gas, such as spiral arms.

VizieR Online Data Catalog: M33 molecular clouds and young stellar clusters (Corbelli+, 2017)

NASA Astrophysics Data System (ADS)

Corbelli, E.; Braine, J.; Bandiera, R.; Brouillet, N.; Combes, F.; Druard, C.; Gratier, P.; Mata, J.; Schuster, K.; Xilouris, M.; Palla, F.

2017-04-01

Table 5 : Physical parameters for the 566 molecular clouds identified through the IRAM 30m CO J=2-1 survey of the star forming disk of M33. For each cloud the cloud type and the following properties are listed: celestial coordinates, galactocentric radius, cloud deconvolved effective radius and its uncertainty, CO(2-1) line velocity dispersion from CPROPS and its uncertainty, line velocity dispersion from a Gaussian fit, CO luminous mass and its uncertainty, and virial mass from a Gaussian fit. In the last column the identification number of the young stellar cluster candidates associated with the molecular cloud are listed. Notes: We identify up to four young stellar cluster candidates (YSCCs) associated with each molecular cloud and we list them according to the identification number of Sharma et al. (2011, Cat. J/A+A/545/A96) given also in Table 6. Table 6 : Physical parameters for the 630 young stellar cluster candidates identified via their mid-infrared emission in the star forming disk of M33. For each YSCC we list the type of source, the identified number of the molecular clouds associated with it (if any) and the corresponding cloud classes. In addition, for each YSCC we give the celestial coordinates, the bolometric, total infrared, FUV and Halpha luminosities, the estimated mass and age, the visual extinction, the galactocentric radius, the source size, and its flux at 24μm. (2 data files).

Molecular Abundances in the Disk of AN Active Galactic Nucleus

NASA Astrophysics Data System (ADS)

Harada, N.; Thompson, T. A.; Herbst, E.

2011-06-01

There are galactic nuclei that emit high luminosities L˜1044-46 erg S-1 including luminosity produced by X-rays from high mass accretion onto the central black holes. These nuclei are called active galactic nuclei (AGNs), and they are accompanied by molecular disks. Observations show high abundances of CN and HCN in the disks; the molecules are proposed to be probes of X-ray dominated regions (XDRs) created by the X-rays from AGNs. We have constructed a spatially-dependent chemical-abundance model of the molecular disk in NGC 1068, a typical AGN-dominated galaxy. Recently, new observations of CN and HCN have been made at much higher spatial resolution, and there are also detections of polyatomic molecules such as HC3N, c-C3H2, and C2H. We discuss how these observations and our simulations can help us to better understand the physical conditions, the disk structure, and conditions for star formation within molecular disks, which are still uncertain. We also include a comparison with other types of galaxies such as (ultra-) luminous infrared galaxies. Usero et al.Astronomy and Astrophysics. 419 (897), 2004. Initial results were presented at the International Symposium on Molecular Spectroscopy 2010, RF05 Garcia-Burillo et al. Astronomy and Astrophysics. 519 (2), 2010. Garcia-Burillo et al. Journal of Physics Conference Series, 131 (12031), 2008. Costagliola et al. ArXiv e-print arXiv:1101.2122, 2011. Nakajima et al. Astrophysical Journal Letters 728 (L38), 2008.

Effects of molecular dissociation on the hydrogen equation of state

NASA Astrophysics Data System (ADS)

Bonev, Stanimir; Schwegler, Eric; Galli, Giulia; Gygi, Francois

2002-03-01

It has been suggested recently(François Gygi and G. Galli, submitted to Phys. Rev. Lett.) that the physical mechanism behind the larger compressibility of liquid deuterium observed in laser shock experiments as compared to ab initio simulations may be related to shock-induced electronic excitations. A possible result of such non-adiabatic processes is hindering of the molecular dissociation. This has motivated us to study the importance of molecular dissociation on the hydrogen equation of state. To this end, we have carried out ab initio molecular dynamics simulations of liquid deuterium where intramolecular dissociation is prevented by the use of bond length contraints. Simulations at both fixed thermodynamic conditions and dynamical simulations of shocked deuterium will be discussed.

A Splash to Nano-Sized Inorganic Energy-Materials by the Low-Temperature Molecular Precursor Approach.

PubMed

Driess, Matthias; Panda, Chakadola; Menezes, Prashanth Wilfried

2018-05-07

The low-temperature synthesis of inorganic materials and their interfaces at the atomic and molecular level provides numerous opportunities for the design and improvement of inorganic materials in heterogeneous catalysis for sustainable chemical energy conversion or other energy-saving areas. Using suitable molecular precursors for functional inorganic nanomaterial synthesis allows for facile control over uniform particle size distribution, stoichiometry, and leads to desired chemical and physical properties. This minireview outlines some advantages of the molecular precursor approach in light of selected recent developments of molecule-to-nanomaterials synthesis for renewable energy applications, relevant for the oxygen evolution reaction (OER), hydrogen evolution reaction (HER) and overall water-splitting. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Low Molecular Weight Chitosan–Insulin Polyelectrolyte Complex: Characterization and Stability Studies

PubMed Central

Al-Kurdi, Zakieh I.; Chowdhry, Babur Z.; Leharne, Stephen A.; Al Omari, Mahmoud M. H.; Badwan, Adnan A.

2015-01-01

The aim of the work reported herein was to investigate the effect of various low molecular weight chitosans (LMWCs) on the stability of insulin using USP HPLC methods. Insulin was found to be stable in a polyelectrolyte complex (PEC) consisting of insulin and LMWC in the presence of a Tris-buffer at pH 6.5. In the presence of LMWC, the stability of insulin increased with decreasing molecular weight of LMWC; 13 kDa LMWC was the most efficient molecular weight for enhancing the physical and chemical stability of insulin. Solubilization of insulin-LMWC polyelectrolyte complex (I-LMWC PEC) in a reverse micelle (RM) system, administered to diabetic rats, results in an oral delivery system for insulin with acceptable bioactivity. PMID:25830681

The emergence of complex behaviours in molecular magnetic materials.

PubMed

Goss, Karin; Gatteschi, Dante; Bogani, Lapo

2014-09-14

Molecular magnetism is considered an area where magnetic phenomena that are usually difficult to demonstrate can emerge with particular clarity. Over the years, however, less understandable systems have appeared in the literature of molecular magnetic materials, in some cases showing features that hint at the spontaneous emergence of global structures out of local interactions. This ingredient is typical of a wider class of problems, called complex behaviours, where the theory of complexity is currently being developed. In this perspective we wish to focus our attention on these systems and the underlying problematic that they highlight. We particularly highlight the emergence of the signatures of complexity in several molecular magnetic systems, which may provide unexplored opportunities for physical and chemical investigations.

Sampling of Protein Folding Transitions: Multicanonical Versus Replica Exchange Molecular Dynamics.

PubMed

Jiang, Ping; Yaşar, Fatih; Hansmann, Ulrich H E

2013-08-13

We compare the efficiency of multicanonical and replica exchange molecular dynamics for the sampling of folding/unfolding events in simulations of proteins with end-to-end β -sheet. In Go-model simulations of the 75-residue MNK6, we observe improvement factors of 30 in the number of folding/unfolding events of multicanonical molecular dynamics over replica exchange molecular dynamics. As an application, we use this enhanced sampling to study the folding landscape of the 36-residue DS119 with an all-atom physical force field and implicit solvent. Here, we find that the rate-limiting step is the formation of the central helix that then provides a scaffold for the parallel β -sheet formed by the two chain ends.

Manipulation of individual hyperfine states in cold trapped molecular ions and application to HD+ frequency metrology.

PubMed

Bressel, U; Borodin, A; Shen, J; Hansen, M; Ernsting, I; Schiller, S

2012-05-04

Advanced techniques for manipulation of internal states, standard in atomic physics, are demonstrated for a charged molecular species for the first time. We address individual hyperfine states of rovibrational levels of a diatomic ion by optical excitation of individual hyperfine transitions, and achieve controlled transfer of population into a selected hyperfine state. We use molecular hydrogen ions (HD+) as a model system and employ a novel frequency-comb-based, continuous-wave 5  μm laser spectrometer. The achieved spectral resolution is the highest obtained so far in the optical domain on a molecular ion species. As a consequence, we are also able to perform the most precise test yet of the ab initio theory of a molecule.

APEX Detection of Molecular Gas in Ram-Pressure Stripped Galaxies

NASA Astrophysics Data System (ADS)

Moretti, Alessia

2017-11-01

I will report on our recent study aimed at detecting molecular gas in the main body and in the tails of a sample of 5 jellyfish galaxies that have been observed within our ongoing MUSE Large Program (GASP). The analyzed sample is constituted by the most extreme jellyfish galaxies, for which the analysis of the ionized gas has already demonstrated that the mechanism at play in regulating 5the gas outflow is the ram pressure stripping. The detection of molecular gas in the tails and the broad characterization that we have been able to extract with APEX data is one of the key ingredients to understand if and how the molecular gas is subject to the same physical process.

Revealing the Physical Properties of GMC Complexes in the Spiral Arms of NGC 6946

NASA Astrophysics Data System (ADS)

Topal, Selçuk; Bayet, Estelle; Bureau, Martin; Walsh, Wilfred; Davis, Timothy A.

2013-03-01

In this study, we probe for the first time the molecular gas physical properties of several star forming regions located in the arms and inter-arms of the spiral galaxy NGC 6946. Combining our observations with additional data found in the literature, we provide in this study the most complete CO ladder ever obtained in these inter-arm and arm regions, i.e. the CO(1-0, 2-1, 3-2, 4-3, 6-5) and 13CO(1-0, 2-1) transitions. For each region studied, we use more precisely the large velocity gradient (LVG) assumption in order to derive the beam-averaged molecular gas physical properties. Namely, we obtained the gas kinetic temperature (i.e. 'best' T K), volume number gas density (i.e. 'best' n(H2)) and CO column density (i.e. 'best' N(CO)) which best reproduce the data for 8 regions investigated. Optical depths were also estimated for a large variety of CO lines in these regions. To identify the best values found, we used two complementary theoretical approaches when comparing the model predictions with the observations, i.e. the χ2 minimisation and the likelihood. Very different physical conditions for the molecular gas from a region to another have been obtained: T K ranges from 10 to 250 K, n(H2) ranges from 102.3 to 107.0 cm-3 and N(CO) ranges from 1015.0 to 1019.3 cm-2 among the arm and inter-arm regions. For each region probed, we also published for the first time the CO spectral line energy distribution (SLED) from CO(1-0) to CO(10-9) for this galaxy, mixing observations and model predictions which provide an essential insight for future follow-up observational programmes. Finally, in this work, we discuss the physical properties we obtained for each region in relation with the presence of young stellar population characteristics such as supernovae remnants (SNRs), Hi holes, Hii regions.

Molecular mobility in amorphous state: Implications on physical stability

NASA Astrophysics Data System (ADS)

Bhardwaj, Sunny Piyush

Amorphous pharmaceuticals are desirable in drug development due to their advantageous biopharmaceutical properties of higher apparent aqueous solubility and dissolution rate. The main obstacle in their widespread use, however, is their higher physicochemical instability than their crystalline counterparts. The goal of the present research project was to investigate correlations between the molecular mobility and physical stability in model amorphous compounds. The objective was to identify the specific mobility which is responsible for the physical instability in each case. This will potentially enable the development of effective strategies for the stabilization of amorphous pharmaceuticals. Moreover, these correlations can be used to develop predictive models for the stability at the pharmaceutically relevant storage conditions. Subtraction of dc conductivity enabled the comprehensive characterization of molecular mobility in amorphous trehalose. This was followed by investigation of correlation between crystallization behavior and different relaxations. Global mobility was found to be strongly coupled to both crystallization onset time and rate. Different preparation methods imparted different mobility states to amorphous trehalose which was postulated to be the reason for the significant physical stability differences. Predictive models were developed and a good agreement was found between the predicted and the experimental crystallization onset times at temperatures around and below the glass transition temperature (Tg). Effect of annealing was investigated on water sorption, enthalpic recovery and dielectric relaxation times in amorphous trehalose. Global mobility was found to be linearly correlated to the water sorption potential which enabled the development of predictive models. Global mobility was also found to be strongly correlated to physical instability in amorphous itraconazole. Effect of polymer (PVP and HPMCAS) on itraconazole mobility and stability was also evaluated. Global mobility was found to be correlated to stability in both the solid dispersions. HPMCAS was found to be a better stabilizer than PVP due to its pronounced effect on global mobility.

Astronomy-inspired Atomic and Molecular Physics

NASA Astrophysics Data System (ADS)

Rau, A. R. P.

2002-02-01

Aimed at senior undergraduate and first-year graduate students in departments of physics and astronomy, this textbook gives a systematic treatment of atomic and molecular structure and spectra, together with the effect of weak and strong external electromagnetic fields. Topics chosen are those of interest in astronomy and indeed many were inspired by specific astronomical contexts. Examples include the negative ion of hydrogen and the effects of strong magnetic fields such as those occurring on certain white dwarfs and neutron stars. Adiabatic and non-adiabatic handling of electron correlations and application to processes such as dielectronic recombination are included. Astronomical examples are provided throughout as well as end-of-the chapter problems and exercises. Over seventy illustrative diagrams complete this unique and comprehensive volume. Link: http://www.wkap.nl/prod/b/1-4020-0467-2

Application of Dirac's Generalized Hamiltonian Dynamics to Atomic and Molecular Systems

NASA Astrophysics Data System (ADS)

Uzer, Turgay

2002-10-01

Incorporating electronic degrees of freedom into classical treatments of atoms and molecules is a challenging problem from both the practical and fundamental points of view. Because it goes to the heart of classical-quantal correspondence, there are now a number of prescriptions which differ by the extent of quantal information that they include. We reach back to Dirac for inspiration, who, half a century ago, designed a so-called Generalized Hamiltonian Dynamics (GHD) with applications to field theory in mind. Physically, the GHD is a purely classical formalism for systems with constraints; it incorporates the constraints into the Hamiltonian. We apply the GHD to atomic and molecular physics by choosing integrals of motion as the constraints. We show that this purely classical formalism allows the derivation of energies of non-radiating states.

Common Principles of Molecular Electronics and Nanoscale Electrochemistry.

PubMed

Bueno, Paulo Roberto

2018-05-24

The merging of nanoscale electronics and electrochemistry can potentially modernize the way electronic devices are currently engineered or constructed. It is well known that the greatest challenges will involve not only miniaturizing and improving the performance of mobile devices, but also manufacturing reliable electrical vehicles, and engineering more efficient solar panels and energy storage systems. These are just a few examples of how technological innovation is dependent on both electrochemical and electronic elements. This paper offers a conceptual discussion of this central topic, with particular focus on the impact that uniting physical and chemical concepts at a nanoscale could have on the future development of electroanalytical devices. The specific example to which this article refers pertains to molecular diagnostics, i.e., devices that employ physical and electrochemical concepts to diagnose diseases.

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.

Membrane bending: the power of protein imbalance.

PubMed

Derganc, Jure; Antonny, Bruno; Copič, Alenka

2013-11-01

Many cellular processes require membrane deformation, which is driven by specialized protein machinery and can often be recapitulated using pure lipid bilayers. However, biological membranes contain a large amount of embedded proteins. Recent research suggests that membrane-bound proteins with asymmetric distribution of mass across the bilayer can influence membrane bending in a nonspecific manner due to molecular crowding. This mechanism is physical in nature and arises from collisions between such 'mushroom-shaped' proteins. It can either facilitate or impede the action of protein coats, for example COPII, during vesicle budding. We describe the physics of how molecular crowding can influence membrane bending and discuss the implications for other cellular processes, such as sorting of glycosylphosphatidylinositol-anchored proteins (GPI-APs) and production of intraluminal vesicles. Copyright © 2013 Elsevier Ltd. All rights reserved.

Pulsed-discharge carbon dioxide lasers

NASA Technical Reports Server (NTRS)

Willetts, David V.

1990-01-01

The purpose is to attempt a general introduction to pulsed carbon dioxide lasers of the kind used or proposed for laser radar applications. Laser physics is an excellent example of a cross-disciplinary topic, and the molecular spectroscopy, energy transfer, and plasma kinetics of the devices are explored. The concept of stimulated emission and population inversions is introduced, leading on to the molecular spectroscopy of the CO2 molecule. This is followed by a consideration of electron-impact pumping, and the pertinent energy transfer and relaxation processes which go on. Since the devices are plasma pumped, it is necessary to introduce a complex subject, but this is restricted to appropriate physics of glow discharges. Examples of representative devices are shown. The implications of the foregoing to plasma chemistry and gas life are discussed.

2D Quantum Simulation of MOSFET Using the Non Equilibrium Green's Function Method

NASA Technical Reports Server (NTRS)

Svizhenko, Alexel; Anantram, M. P.; Govindan, T. R.; Yan, Jerry (Technical Monitor)

2000-01-01

The objectives this viewgraph presentation summarizes include: (1) the development of a quantum mechanical simulator for ultra short channel MOSFET simulation, including theory, physical approximations, and computer code; (2) explore physics that is not accessible by semiclassical methods; (3) benchmarking of semiclassical and classical methods; and (4) study other two-dimensional devices and molecular structure, from discretized Hamiltonian to tight-binding Hamiltonian.

Laboratory directed research and development. FY 1995 progress report

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

Vigil, J.; Prono, J.

1996-03-01

This document presents an overview of Laboratory Directed Research and Development Programs at Los Alamos. The nine technical disciplines in which research is described include materials, engineering and base technologies, plasma, fluids, and particle beams, chemistry, mathematics and computational science, atmic and molecular physics, geoscience, space science, and astrophysics, nuclear and particle physics, and biosciences. Brief descriptions are provided in the above programs.

Kinetic exchange models: From molecular physics to social science

NASA Astrophysics Data System (ADS)

Patriarca, Marco; Chakraborti, Anirban

2013-08-01

We discuss several multi-agent models that have their origin in the kinetic exchange theory of statistical mechanics and have been recently applied to a variety of problems in the social sciences. This class of models can be easily adapted for simulations in areas other than physics, such as the modeling of income and wealth distributions in economics and opinion dynamics in sociology.

Exact symmetries in the velocity fluctuations of a hot Brownian swimmer

NASA Astrophysics Data System (ADS)

Falasco, Gianmaria; Pfaller, Richard; Bregulla, Andreas P.; Cichos, Frank; Kroy, Klaus

2016-09-01

Symmetries constrain dynamics. We test this fundamental physical principle, experimentally and by molecular dynamics simulations, for a hot Janus swimmer operating far from thermal equilibrium. Our results establish scalar and vectorial steady-state fluctuation theorems and a thermodynamic uncertainty relation that link the fluctuating particle current to its entropy production at an effective temperature. A Markovian minimal model elucidates the underlying nonequilibrium physics.

Molecules in interstellar clouds. [physical and chemical conditions of star formation and biological evolution

NASA Technical Reports Server (NTRS)

Irvine, W. M.; Hjalmarson, A.; Rydbeck, O. E. H.

1981-01-01

The physical conditions and chemical compositions of the gas in interstellar clouds are reviewed in light of the importance of interstellar clouds for star formation and the origin of life. The Orion A region is discussed as an example of a giant molecular cloud where massive stars are being formed, and it is pointed out that conditions in the core of the cloud, with a kinetic temperature of about 75 K and a density of 100,000-1,000,000 molecules/cu cm, may support gas phase ion-molecule chemistry. The Taurus Molecular Clouds are then considered as examples of cold, dark, relatively dense interstellar clouds which may be the birthplaces of solar-type stars and which have been found to contain the heaviest interstellar molecules yet discovered. The molecular species identified in each of these regions are tabulated, including such building blocks of biological monomers as H2O, NH3, H2CO, CO, H2S, CH3CN and H2, and more complex species such as HCOOCH3 and CH3CH2CN.

Tensegrity: the architectural basis of cellular mechanotransduction

NASA Technical Reports Server (NTRS)

Ingber, D. E.

1997-01-01

Physical forces of gravity, hemodynamic stresses, and movement play a critical role in tissue development. Yet, little is known about how cells convert these mechanical signals into a chemical response. This review attempts to place the potential molecular mediators of mechanotransduction (e.g. stretch-sensitive ion channels, signaling molecules, cytoskeleton, integrins) within the context of the structural complexity of living cells. The model presented relies on recent experimental findings, which suggests that cells use tensegrity architecture for their organization. Tensegrity predicts that cells are hard-wired to respond immediately to mechanical stresses transmitted over cell surface receptors that physically couple the cytoskeleton to extracellular matrix (e.g. integrins) or to other cells (cadherins, selectins, CAMs). Many signal transducing molecules that are activated by cell binding to growth factors and extracellular matrix associate with cytoskeletal scaffolds within focal adhesion complexes. Mechanical signals, therefore, may be integrated with other environmental signals and transduced into a biochemical response through force-dependent changes in scaffold geometry or molecular mechanics. Tensegrity also provides a mechanism to focus mechanical energy on molecular transducers and to orchestrate and tune the cellular response.

Inelastic electron tunneling mediated by a molecular quantum rotator

NASA Astrophysics Data System (ADS)

Sugimoto, Toshiki; Kunisada, Yuji; Fukutani, Katsuyuki

2017-12-01

Inelastic electron tunneling (IET) accompanying nuclear motion is not only of fundamental physical interest but also has strong impacts on chemical and biological processes in nature. Although excitation of rotational motion plays an important role in enhancing electric conductance at a low bias, the mechanism of rotational excitation remains veiled. Here, we present a basic theoretical framework of IET that explicitly takes into consideration quantum angular momentum, focusing on a molecular H2 rotator trapped in a nanocavity between two metallic electrodes as a model system. It is shown that orientationally anisotropic electrode-rotator coupling is the origin of angular-momentum exchange between the electron and molecule; we found that the anisotropic coupling imposes rigorous selection rules in rotational excitation. In addition, rotational symmetry breaking induced by the anisotropic potential lifts the degeneracy of the energy level of the degenerated rotational state of the quantum rotator and tunes the threshold bias voltage that triggers rotational IET. Our theoretical results provide a paradigm for physical understanding of the rotational IET process and spectroscopy, as well as molecular-level design of electron-rotation coupling in nanoelectronics.

An uncertainty principle for star formation - II. A new method for characterising the cloud-scale physics of star formation and feedback across cosmic history

NASA Astrophysics Data System (ADS)

Kruijssen, J. M. Diederik; Schruba, Andreas; Hygate, Alexander P. S.; Hu, Chia-Yu; Haydon, Daniel T.; Longmore, Steven N.

2018-05-01

The cloud-scale physics of star formation and feedback represent the main uncertainty in galaxy formation studies. Progress is hampered by the limited empirical constraints outside the restricted environment of the Local Group. In particular, the poorly-quantified time evolution of the molecular cloud lifecycle, star formation, and feedback obstructs robust predictions on the scales smaller than the disc scale height that are resolved in modern galaxy formation simulations. We present a new statistical method to derive the evolutionary timeline of molecular clouds and star-forming regions. By quantifying the excess or deficit of the gas-to-stellar flux ratio around peaks of gas or star formation tracer emission, we directly measure the relative rarity of these peaks, which allows us to derive their lifetimes. We present a step-by-step, quantitative description of the method and demonstrate its practical application. The method's accuracy is tested in nearly 300 experiments using simulated galaxy maps, showing that it is capable of constraining the molecular cloud lifetime and feedback time-scale to <0.1 dex precision. Access to the evolutionary timeline provides a variety of additional physical quantities, such as the cloud-scale star formation efficiency, the feedback outflow velocity, the mass loading factor, and the feedback energy or momentum coupling efficiencies to the ambient medium. We show that the results are robust for a wide variety of gas and star formation tracers, spatial resolutions, galaxy inclinations, and galaxy sizes. Finally, we demonstrate that our method can be applied out to high redshift (z≲ 4) with a feasible time investment on current large-scale observatories. This is a major shift from previous studies that constrained the physics of star formation and feedback in the immediate vicinity of the Sun.

Physical Heterogeneity Increases Biofilm Resource Use and Its Molecular Diversity in Stream Mesocosms

PubMed Central

Singer, Gabriel; Besemer, Katharina; Schmitt-Kopplin, Philippe; Hödl, Iris; Battin, Tom J.

2010-01-01

Background Evidence increasingly shows that stream ecosystems greatly contribute to global carbon fluxes. This involves a tight coupling between biofilms, the dominant form of microbial life in streams, and dissolved organic carbon (DOC), a very significant pool of organic carbon on Earth. Yet, the interactions between microbial biodiversity and the molecular diversity of resource use are poorly understood. Methodology/Principal Findings Using six 40-m-long streamside flumes, we created a gradient of streambed landscapes with increasing spatial flow heterogeneity to assess how physical heterogeneity, inherent to streams, affects biofilm diversity and DOC use. We determined bacterial biodiversity in all six landscapes using 16S-rRNA fingerprinting and measured carbon uptake from glucose and DOC experimentally injected to all six flumes. The diversity of DOC molecules removed from the water was determined from ultrahigh-resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry (FTICR-MS). Bacterial beta diversity, glucose and DOC uptake, and the molecular diversity of DOC use all increased with increasing flow heterogeneity. Causal modeling and path analyses of the experimental data revealed that the uptake of glucose was largely driven by physical processes related to flow heterogeneity, whereas biodiversity effects, such as complementarity, most likely contributed to the enhanced uptake of putatively recalcitrant DOC compounds in the streambeds with higher flow heterogeneity. Conclusions/Significance Our results suggest biophysical mechanisms, including hydrodynamics and microbial complementarity effects, through which physical heterogeneity induces changes of resource use and carbon fluxes in streams. These findings highlight the importance of fine-scale streambed heterogeneity for microbial biodiversity and ecosystem functioning in streams, where homogenization and loss of habitats increasingly reduce biodiversity. PMID:20376323

Radiation health research, 1986 - 1990

NASA Technical Reports Server (NTRS)

1991-01-01

A collection of 225 abstracts of radiation research sponsored by NASA during the period 1986 through 1990 is reported. Each abstract was categorized within one of four discipline areas: physics, biology, risk assessment, and microgravity. Topic areas within each discipline were assigned as follows: Physics - atomic physics, nuclear science, space radiation, radiation transport and shielding, and instrumentation; Biology - molecular biology, cellular radiation biology, tissue, organs and organisms, radioprotectants, and plants; Risk assessment - radiation health and epidemiology, space flight radiation health physics, inter- and intraspecies extrapolation, and radiation limits and standards; and Microgravity. When applicable subareas were assigned for selected topic areas. Keywords and author indices are provided.

Science and Technology of Nanostructured Magnetic Materials: Proceedings of a NATO Advanced Study Institute Conference Held in Aghia Pelaghia, Crete, Greece on 24 June -6 July 1990. NATO ASI Series B: Physics. Volume 259

DTIC Science & Technology

1990-07-06

Tung in Silicon-Molecular Beam Epitaxy. vol. 11 eds. Erich Kasper and John C . Bean, CRC Press, Boca Raton, FL (1988), or J. Derrien and F. Arnaud...mum~ J goS-MS AD- A24 6 363 ..T.. C .... Magnetbic Mean eiteral C dstibtio I Edliited.b Gary A . ....... MagntOc aeria Series B: Physics Vol. 259 ’o98...NATO Scientific Affairs Division A Life Sciences Plenum Publishing Corporation B Physics New York and London C Mathematical and Physical Sciences Kluwer

Autonomous Agents: The Origins and Co-Evolution of Reproducing Molecular Systems

NASA Technical Reports Server (NTRS)

Kauffman, Stuart

1999-01-01

The central aim of this award concerned an investigation into, and adequate formulation of, the concept of an "autonomous agent." If we consider a bacterium swimming upstream in a glucose gradient, we are willing to say of the bacterium that it is going to get food. That is, we are willing, and do, describe the bacterium as acting on its own behalf in an environment. All free living cells are, in this sense, autonomous agents. But the bacterium is "just" a set of molecules. We define an autonomous agent as a physical system able to act on its own behalf in an environment, then ask, "What must a physical system be to be an autonomous agent?" The tentative definition for a molecular autonomous agent is that it must be self-reproducing and carry out at least one thermodynamic work cycle. The work carried out in this grant involved, among other features, the development of a detailed model of a molecular autonomous agent, and study of the kinetics of this system. In particular, a molecular autonomous agent must, by the above tentative definition, not only reproduce, but must carry out at least one work cycle. I took, as a simple example of a self-reproducing molecular system, the single-stranded DNA hexamer 3'CCGCGG5' which can line up and ligate its two complementary trimers, 5'CCG3' and 5'CGG3'. But the two ligated trimers constitute the same molecular sequence in the 3' to 5' direction as the initial hexamer, hence this system is autocatalytic. On the other hand the above system is not yet an autonomous agent. At the minimum, autonomous agents, as I have defined them, are a new class of chemical reaction network. At a maximum, they may constitute a proper definition of life itself.

Obituary: Alexander Dalgarno (1928 - 2015)

NASA Astrophysics Data System (ADS)

Hartquist, Tom; Babb, James F. Babb; Loeb, Avi

Alex Dalgarno's major contributions to the understanding of fundamental atomic and molecular processes enabled him to develop diagnostics of the physical conditions of atmospheres and astrophysical sources and to elucidate the roles of such processes in controlling those environments. He greatly influenced the research of physicists, chemists, atmospheric scientists, and astronomers, leading Sir David Bates to write, "There is no greater figure than Alex in the history of atomic physics and its applications." Alex was born and grew up in London. As a child, he enjoyed mathematical puzzles and did well at sports. He was invited to try out for the Tottenham Hotspur soccer team, but his professional sporting career ended due to an injury, which did not prevent Alex playing tennis and squash into his ninth decade. In 1945 Alex began to study Mathematics at University College London (UCL). In 1947 Sir Harrie Massey invited him to work for a PhD in Physics and suggested that Alex investigate collisions of metastable helium atoms in helium gas to determine the cross sections for excitation transfer. Richard Buckingham was Alex's immediate supervisor. After completing his graduate study in 1951, Alex became a member of staff in Applied Mathematics at the Queen's University of Belfast (QUB). He served as the Director of the Computational Laboratory after a 1954 visit to MIT, which had an electronic computer, led Alex to persuade colleagues that QUB needed one. In 1957, the poet Philip Larkin was the best man at the marriage of Alex to Barbara Kane. They had four children, Fergus, Penelope, Piers, and Rebecca, but the marriage dissolved after ten years. Alex's important work during the 1950s on the quantitative evaluation of long-range interactions underpinned his collaborations on precise scattering calculations relevant to ultra-cold collisions and the formation of atomic Bose-Einstein condensates over four decades later. He investigated the theory of atomic and molecular collisions and calculated charge transfer cross sections. Some of these proved later to be important for forming the spectra of diffuse astronomical matter surrounding high mass stars and 100 million solar mass black holes at the centers of active galaxies. In the early 1950s David Bates stimulated Alex's interest in the study of quantum processes occurring in the upper terrestrial atmosphere. Together they considered the sources of the nightglow and dayglow features and concluded that the altitudes previously inferred for them from observations were up to several hundred kilometers too large. Experiments carried on V2 rockets, like those seen by Alex in wartime London, proved him and David to be right. Alex felt that though many theorists believe that "physics is embodied in its equations," it is instead "to be found in the solutions to the equations." He was a master at developing and applying methods that simplified calculations leading to reliable solutions. Exploiting the contemporary advances in electronic computation, by the 1960s Alex and his colleagues were able to address atomic and molecular processes of increasing complexity. Their development and early applications of the S-matrix theory of molecular rotational excitation by particle impact triggered major advances in molecular physics and theoretical chemistry and in the understanding of processes important in many environments, including a wide variety of astrophysical sources. In 1967 Alex became a professor in the Harvard Department of Astronomy and a member of the staff of the Smithsonian Astrophysical Observatory. He was a team member for several Atmosphere Explorer satellite missions, which elucidated the roles of atoms and ions in the upper atmosphere and paved the way for further applications to the other planets. By 1969 Alex was publishing papers on molecular hydrogen (H2) radiative processes, including photodissociation, in which the foundations of molecular astrophysics began to emerge. H2 is the most abundant astrophysical molecule and the main constituent of the regions where stars form. Interstellar H2 was first detected directly in the following year, and data for interstellar H2 began to become abundant in 1973. Alex was well prepared and led efforts to interpret these data, from which he was able to infer the physical properties of diffuse interstellar molecular clouds. At nearly the same time he was involved in work on the ionization and energy deposition in H2 by nearly relativistic and relativistic particles called cosmic rays. The work has relevance to emission in the atmospheres of the giant planets, as well as for conditions in interstellar molecular clouds. Cosmic ray induced ionization initiates much of the basic chemistry in star forming regions, and the emissions of the product molecules control the temperatures and allow the diagnosis of the physical conditions and dynamics of the stellar nurseries. For more than four decades Alex elucidated the chemical networks governing the molecular abundances in a wide variety of astrophysical sources including star forming regions, supernova ejecta, the pregalactic universe, and extreme environments like those in the vicinities of X-ray sources powered by accretion onto black holes. The refinement of the models led to calculations predicting the existence of subsequently discovered negative ions in giant molecular clouds. One of his astrophysical interests that intrigued him late in his career was the emission of soft X-rays by comets and in the heliosphere due to charge transfer with solar wind particles, and he also worked on related processes occurring in the atmospheres of the giant planets. Alex remained very active in fundamental atomic and molecular physics, as well as for its applications to astrophysics and to terrestrial and extraterrestrial planetary atmospheres. Ultra-cold collisions and ultra-cold chemistry were major interests for Alex for much of the latest phase of his career, most recently with pioneering work on atom-molecule collisions. In the early 1980s Alex had concerns about the future of atomic, molecular, and optical (AMO) physics in the United States, where it was inadequately funded and somewhat out of fashion in many of the physics departments providing most of the physicists who became university faculty. Alex played a key role in efforts to address this issue and led a proposal to the National Science Foundation that resulted in the founding on 1 November 1988 of the Institute of Theoretical Atomic and Molecular Physics (ITAMP) at the Harvard-Smithsonian Center for Astrophysics. Alex served for five years as the first ITAMP director. A number of the former ITAMP students and postdoctoral researchers have become leading AMO physicists, and its visitor program and workshops have led to the identification and stimulation of the leading areas of AMO physics. Alex was a Fellow of the Royal Society, a member of the National Academy of Sciences, and a member (Honorary) of the Royal Irish Academy. He received many medals, including the Benjamin Franklin Medal in Physics, the Royal Society's Hughes Medal, the Royal Astronomical Society's Gold Medal, the American Geophysical Society's Fleming Medal, and the Royal Society of Chemistry's Spiers Medal. He served as the editor of the Astrophysical Journal Letters for nearly thirty years starting in 1973, as the Chair of the Harvard Department of Astronomy from 1971 to 1976, and as the Acting Director of Harvard College Observatory and then the Acting Director of the Harvard-Smithsonian Center for Astrophysics from 1971 to 1973 during a critical period of its existence. Alex was a gifted mentor who spoke and wrote with pride of his former students and postdoctoral researchers. He was able to match projects very well with the abilities of the students. He made availability to students a special priority, and despite his supply of problems would encourage students as they developed their own. Alex was very supportive of junior scientists as they developed their careers, and in addition to writing many letters of recommendation he made many visits to colleagues as they were establishing themselves elsewhere. Furthermore, Alex very graciously hosted a number of his former students when they visited. He combined quiet modesty with a confidence that reassured others, and his humor was dry, interactive, and friendly. Alex passed away peacefully on 9 April 2015 in Cambridge, Massachusetts in the company of Fern Creelan, who was his partner for 30 years.

Characterization and analysis of the molecular weight of lignin for biorefining studies

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

Tolbert, Allison; Akinosho, Hannah; Khunsupat, Ratayakorn

2014-06-04

The molecular weight of lignin is a fundamental property that infl uences the recalcitrance of biomass and the valorization of lignin. The determination of the molecular weight of lignin in native biomass is dependent on the bioresources used and the isolation and purifi cation procedures employed. The three most commonly employed isolation methods are milled wood lignin (MWL), cellulolytic enzyme lignin (CEL), and enzymatic mild acidolysis lignin (EMAL). Common characterization techniques for determining the molecular weight of lignin will be addressed, with an emphasis on gel permeation chromatography (GPC). This review also examines the mechanisms behind several biological, physical, andmore » chemical pre-treatments and their impact on the molecular weight of lignin. The number average molecular weight (Mn), weight average molecular weight (Mw) and polydispersity index (D) all vary in magnitude depending on the biomass source, pre-treatment conditions, and isolation method. Additionally, there is a growing body of literature that supports changes in the molecular weight of lignin in response to genetic modifi cations in the lignin biosynthetic pathways. This review summarizes different procedures for obtaining the molecular weight of lignin that have been used in recent years and highlight future opportunities for applications of lignin.« less

Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics

NASA Astrophysics Data System (ADS)

Wehmeyer, Christoph; Noé, Frank

2018-06-01

Inspired by the success of deep learning techniques in the physical and chemical sciences, we apply a modification of an autoencoder type deep neural network to the task of dimension reduction of molecular dynamics data. We can show that our time-lagged autoencoder reliably finds low-dimensional embeddings for high-dimensional feature spaces which capture the slow dynamics of the underlying stochastic processes—beyond the capabilities of linear dimension reduction techniques.

Physical conditions of the molecular gas in metal-poor galaxies

NASA Astrophysics Data System (ADS)

Hunt, L. K.; Weiß, A.; Henkel, C.; Combes, F.; García-Burillo, S.; Casasola, V.; Caselli, P.; Lundgren, A.; Maiolino, R.; Menten, K. M.; Testi, L.

2017-10-01

Studying the molecular component of the interstellar medium (ISM) in metal-poor galaxies has been challenging because of the faintness of carbon monoxide emission, the most common proxy of H2. Here we present new detections of molecular gas at low metallicities, and assess the physical conditions in the gas through various CO transitions for 8 galaxies. For one, NGC 1140 (Z/Z⊙ 0.3), two detections of 13CO isotopologues and atomic carbon, [Ci](1-0) and an upper limit for HCN(1-0) are also reported. After correcting to a common beam size, we compared 12CO(2-1)/12CO(1-0) (R21) and 12CO(3-2)/12CO(1-0) (R31) line ratios of our sample with galaxies from the literature and find that only NGC 1140 shows extreme values (R21 R31 2). Fitting physical models to the 12CO and 13CO emission in NGC 1140 suggests that the molecular gas is cool (kinetic temperature Tkin ≲ 20 K), dense (H2 volume density nH2 ≳ 106 cm-3), with moderate CO column density (NCO 1016 cm-2) and low filling factor. Surprisingly, the [12CO]/[13CO] abundance ratio in NGC 1140 is very low ( 8-20), lower even than the value of 24 found in the Galactic Center. The young age of the starburst in NGC 1140 precludes 13CO enrichment from evolved intermediate-mass stars; instead we attribute the low ratio to charge-exchange reactions and fractionation, because of the enhanced efficiency of these processes in cool gas at moderate column densities. Fitting physical models to 12CO and [Ci](1-0) emission in NGC 1140 gives an unusually low [12CO]/[12C] abundance ratio, suggesting that in this galaxy atomic carbon is at least 10 times more abundant than 12CO. Based on observations carried out with the IRAM 30 m and the Atacama Pathfinder Experiment (APEX). IRAM is supported by the INSU/CNRS (France), MPG (Germany), and IGN (Spain), and APEX is a collaboration between the Max-Planck-Institut fur Radioastronomie, the European Southern Observatory, and the Onsala Space Observatory.

PREFACE: XXV International Conference on Photonic, Electronic and Atomic Collisions

NASA Astrophysics Data System (ADS)

Becker, Uwe; Moshammer, Robert; Mokler, Paul; Ullrich, Joachim

2007-07-01

The XXVth ICPEAC in Freiburg marked a notable anniversary in collision physics: half a century ago the first conference in the series of International Conferences on the Physics of Electronic and Atomic Collisions (ICPEAC) was held in New York (1958). Since then, the development of electronic and atomic collision physics has seen tremendous progress. Starting during a time, when this field was regarded as somehow out-of-date, certainly not being in the main stream compared to particle and high-energy physics, it has expanded in a rather exceptional and unforeseen way. Over the years the original scope on electronic, atomic and heavy-ion collision physics was extended substantially to include upcoming expanding fields like synchrotron-radiation and strong-field laser-based atomic and molecular physics giving rise to a change of name to 'Photonic', Electronic and Atomic Collisions (ICPEAC) being used for the first time for the ICPEAC in Santa Fee in 2001. Nowadays, the ICPEAC has opened its agenda even more widely to other fields of atomic and molecular physics, such as interactions with clusters, bio-molecules and surfaces, to cold collisions, coherent control, femto- and attosecond physics and, with the Freiburg conference, to the application of free-electron lasers in the vacuum ultraviolet and soft x-ray regime, a field of potentially huge future impact in essentially all areas of science. In this larger context the XXVth ICPEAC in Freiburg with more than 800 participants set new standards. Representatives from all fields of Atomic, Molecular and Photon-based science came together and had very fruitful, inter-disciplinary discussions. This new forum of collision-based AMP physics will serve as a showcase example of future conferences, bridging not only the gap between different fields of collision physics but also, equally important, between different continents and cultures. The next ICPEAC is going to take place in Kalamazoo in North America, the one after that in Belfast back in Europe, and the subsequent one, 2013 in Lanzhou, will be the first one ever held in China. A great perspective for this ever-growing field of science! Uwe Becker (Fritz-Haber-Institut, Berlin) Robert Moshammer (Max-Planck-Institut für Kernphysik, Heidelberg) Paul Mokler (Gesellschaft für Schwerionenforschung, Darmstadt) Joachim Ullrich (Max-Planck-Institut für Kernphysik, Heidelberg) Editors Relaxed atmosphere for discussions during coffee breaks at ICPEAC XXV in Freiburg. The PDF file contains details of previous conferences, sponsors, exhibitors and committees.

Molecular Rift: Virtual Reality for Drug Designers.

PubMed

Norrby, Magnus; Grebner, Christoph; Eriksson, Joakim; Boström, Jonas

2015-11-23

Recent advances in interaction design have created new ways to use computers. One example is the ability to create enhanced 3D environments that simulate physical presence in the real world--a virtual reality. This is relevant to drug discovery since molecular models are frequently used to obtain deeper understandings of, say, ligand-protein complexes. We have developed a tool (Molecular Rift), which creates a virtual reality environment steered with hand movements. Oculus Rift, a head-mounted display, is used to create the virtual settings. The program is controlled by gesture-recognition, using the gaming sensor MS Kinect v2, eliminating the need for standard input devices. The Open Babel toolkit was integrated to provide access to powerful cheminformatics functions. Molecular Rift was developed with a focus on usability, including iterative test-group evaluations. We conclude with reflections on virtual reality's future capabilities in chemistry and education. Molecular Rift is open source and can be downloaded from GitHub.

Stability of high-mass molecular libraries: the role of the oligoporphyrin core

PubMed Central

Sezer, Uĝur; Schmid, Philipp; Felix, Lukas; Mayor, Marcel; Arndt, Markus

2015-01-01

Molecular beam techniques are a key to many experiments in physical chemistry and quantum optics. In particular, advanced matter-wave experiments with high-mass molecules profit from the availability of slow, neutral and mass-selected molecular beams that are sufficiently stable to remain intact during laser heating and photoionization mass spectrometry. We present experiments on the photostability with molecular libraries of tailored oligoporphyrins with masses up to 25 000 Da. We compare two fluoroalkylsulfanyl-functionalized libraries based on two different molecular cores that offer the same number of anchor points for functionalization but differ in their geometry and electronic properties. A pentaporphyrin core stabilizes a library of chemically well-defined molecules with more than 1600 atoms. They can be neutrally desorbed with velocities as low as 20 m/s and efficiently analyzed in photoionization mass spectrometry. Copyright © 2015 John Wiley & Sons, Ltd. PMID:25601698

Superoxide dismutase from Trichuris ovis--inhibition by benzimidazoles and pyrimidine derivatives.

PubMed

Sanchez-Moreno, M; Garcia-Rejon, L; Salas, I; Osuna, A; Monteoliva, M

1992-01-01

Three superoxide dismutase isoenzymes of different cellular location were detected in an homogenate of Trichuris ovis. Each of these molecular forms was purified by differential centrifugation and precipitation with ammonium sulphate, followed by chromatography on DEAE-cellulose and Sephadex G-75 columns. The activity levels of the two molecular forms detected in the mitochondrial (one cyanide sensitive Cu-Zn-SOD and the other cyanide insensitive Mn-SOD) were higher than that of the superoxide dismutase detected in the cytoplasmic fraction (cyanide sensitive Cu-Zn-SOD). All molecular forms present evident differences to the SODs contained in the host liver. Molecular mass and some of the physical and chemical properties of the enzyme was determined for all three molecular forms. An inhibitory effect on the SOD of the parasite an the host was detected with a series of compounds, some of which markedly inhibited parasite enzyme but not host enzyme.

Open-Shell-Character-Based Molecular Design Principles: Applications to Nonlinear Optics and Singlet Fission.

PubMed

Nakano, Masayoshi

2017-01-01

Open-shell character, e. g., diradical character, is a quantum chemically well-defined quantity in ground-state molecular systems, which is not an observable but can quantify the degree of effective bond weakness in the chemical sense or electron correlation strength in the physical sense. Because this quantity also correlates to specific excited states, physicochemical properties concerned with those states are expected to strongly correlate to the open-shell character. This feature enables us to open a new path to revealing the mechanism of these properties as well as to realizing new design principles for efficient functional molecular systems. This account explains the open-shell-character-based molecular design principles and introduces their applications to the rational design of highly efficient nonlinear optical and singlet fission molecular systems. © 2017 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems.

PubMed

Niethammer, Christoph; Becker, Stefan; Bernreuther, Martin; Buchholz, Martin; Eckhardt, Wolfgang; Heinecke, Alexander; Werth, Stephan; Bungartz, Hans-Joachim; Glass, Colin W; Hasse, Hans; Vrabec, Jadran; Horsch, Martin

2014-10-14

The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales that were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multicenter rigid potential models based on Lennard-Jones sites, point charges, and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, such as fluids at interfaces, as well as nonequilibrium molecular dynamics simulation of heat and mass transfer.

Manipulation of Molecular Weight Distribution Shape as a New Strategy to Control Processing Parameters.

PubMed

Nadgorny, Milena; Gentekos, Dillon T; Xiao, Zeyun; Singleton, S Parker; Fors, Brett P; Connal, Luke A

2017-10-01

Molecular weight and dispersity (Ð) influence physical and rheological properties of polymers, which are of significant importance in polymer processing technologies. However, these parameters provide only partial information about the precise composition of polymers, which is reflected by the shape and symmetry of molecular weight distribution (MWD). In this work, the effect of MWD symmetry on thermal and rheological properties of polymers with identical molecular weights and Ð is demonstrated. Remarkably, when the MWD is skewed to higher molecular weight, a higher glass transition temperature (T g ), increased stiffness, increased thermal stability, and higher apparent viscosities are observed. These observed differences are attributed to the chain length composition of the polymers, easily controlled by the synthetic strategy. This work demonstrates a versatile approach to engineer the properties of polymers using controlled synthesis to skew the shape of MWD. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Foundational concepts and underlying theories for majors in "biochemistry and molecular biology".

PubMed

Tansey, John T; Baird, Teaster; Cox, Michael M; Fox, Kristin M; Knight, Jennifer; Sears, Duane; Bell, Ellis

2013-01-01

Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members and science educators from around the country that focused on identifying: 1) core principles of biochemistry and molecular biology, 2) essential concepts and underlying theories from physics, chemistry, and mathematics, and 3) foundational skills that undergraduate majors in biochemistry and molecular biology must understand to complete their major coursework. Using information gained from these workshops, as well as from the ASBMB accreditation working group and the NSF Vision and Change report, the Core Concepts working group has developed a consensus list of learning outcomes and objectives based on five foundational concepts (evolution, matter and energy transformation, homeostasis, information flow, and macromolecular structure and function) that represent the expected conceptual knowledge base for undergraduate degrees in biochemistry and molecular biology. This consensus will aid biochemistry and molecular biology educators in the development of assessment tools for the new ASBMB recommended curriculum. © 2013 by The International Union of Biochemistry and Molecular Biology.

Scanning number and brightness yields absolute protein concentrations in live cells: a crucial parameter controlling functional bio-molecular interaction networks.

PubMed

Papini, Christina; Royer, Catherine A

2018-02-01

Biological function results from properly timed bio-molecular interactions that transduce external or internal signals, resulting in any number of cellular fates, including triggering of cell-state transitions (division, differentiation, transformation, apoptosis), metabolic homeostasis and adjustment to changing physical or nutritional environments, amongst many more. These bio-molecular interactions can be modulated by chemical modifications of proteins, nucleic acids, lipids and other small molecules. They can result in bio-molecular transport from one cellular compartment to the other and often trigger specific enzyme activities involved in bio-molecular synthesis, modification or degradation. Clearly, a mechanistic understanding of any given high level biological function requires a quantitative characterization of the principal bio-molecular interactions involved and how these may change dynamically. Such information can be obtained using fluctation analysis, in particular scanning number and brightness, and used to build and test mechanistic models of the functional network to define which characteristics are the most important for its regulation.

Fast molecular shocks. I - Reformation of molecules behind a dissociative shock

NASA Technical Reports Server (NTRS)

Neufeld, David A.; Dalgarno, A.

1989-01-01

The physical and chemical processes that operate in the cooling gas behind a fast, dissociative, single-fluid shock propagating in a dense interstellar cloud are discussed. The treatment extends previous theoretical work on fast molecular shocks by including the effects of the conversion of Ly-alpha photons into radiation of the two-photon continuum and into H2 Lyman band emission lines, the effects of CO photodissociation following line absorption, and the formation and destruction of molecules containing the elements nitrogen, silicon, and sulphur, and of the complex hydrocarbons. Abundance profiles for the molecular species of interest are presented. After molecular hydrogen begins to reform, by means of gas phase and grain surface processes, the neutral species OH, H2O, O2, CO, CN, HCN, N2, NO, SO, and SiO reach substantial abundances. The molecular ions HeH(+), OH(+), SO(+), CH(+), H2(+), and H3(+), are produced while the gas is still hot and partially ionized. Emissions from them provide a possible diagnostic probe of fast molecular shocks.

Premier Tools of Energy Research Also Probe Secrets of Viral Disease

DOE R&D Accomplishments Database

Chui, Glennda

2011-03-28

Advanced light sources peer into matter at the atomic and molecular scales, with applications ranging from physics, chemistry, materials science, and advanced energy research, to biology and medicine.

Controlled, Site-Specific Functionalization of Carbon Nanotubes with Diazonium Salts

NASA Technical Reports Server (NTRS)

Tour, James M.

2013-01-01

This work uses existing technologies to prepare a crossbar architecture of nano tubes, wherein one nanotube is fixed to a substrate, and a second nanotube is suspended a finite distance above. Both nano tubes can be individually addressed electrically. Application of opposite potentials to the two tubes causes the top tube to deform and to essentially come into contact with the lower tube. Contact here refers not to actual, physical contact, but rather within an infinitesimally small distance referred to as van der Walls contact, in which the entities may influence each other on a molecular and electronic scale. First, the top tube is physically deformed, leading to a potentially higher chemical reactivity at the point of deformation, based on current understanding of the effects of curvature strain on reactivity. This feature would allow selective functionalization at the junction via reaction with diazonium salts. Secondly, higher potential is achieved at the point of "cross" between the tubes. In a pending patent application, a method is claimed for directed self-assembly of molecular components onto the surface of metal or conductive materials by application of potential to the metal or conductive surface. In another pending patent application, a method is claimed for attaching molecules to the surface of nanotubes via the use of reactive diazonium salts. In the present invention, the directed functionalization of the crossed-nanotube junctions by applying a potential to the ends of the nanotubes in the presence of reactive diazonium slats, or other reactive molecular species is claimed. The diazonium salts are directed by the potential existing at the junction to react with the surface of the nanotube, thus placing functional molecular components at the junctions. The crossed nano tubes therefore provide a method of directly addressing the functionalized molecules, which have been shown to function as molecular switches, molecular wires, and in other capacities and uses. Site-specific functionalization may enable the use of nanotubes in molecular electronic applications because device functionality is critical at the cross points.

Design theory and performance of cryogenic molecular adsorption refrigeration systems

NASA Technical Reports Server (NTRS)

Hartwig, W. H.; Woltman, A. W.; Masson, J. P.

1978-01-01

Closed-cycle operation of molecular adsorption refrigeration systems (MARS) has been demonstrated by using thermally cycled zeolites to adsorb and desorb various gases under pressures of 20-60 atm. This paper develops three aspects of the design theory: the physical theory of molecular adsorption of small molecules such as A, N2, N2O and NH3, the design relations for closed-cycle flow for three or more compressors, and the coefficient of performance. This work is intended to demonstrate nonmechanical gas compression for various cryogenic gases than can compete with mechanical systems with a different mix of advantages and disadvantages.

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.

PubMed

Šponer, Jiří; Banáš, Pavel; Jurečka, Petr; Zgarbová, Marie; Kührová, Petra; Havrila, Marek; Krepl, Miroslav; Stadlbauer, Petr; Otyepka, Michal

2014-05-15

We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.

A centroid molecular dynamics study of liquid para-hydrogen and ortho-deuterium.

PubMed

Hone, Tyler D; Voth, Gregory A

2004-10-01

Centroid molecular dynamics (CMD) is applied to the study of collective and single-particle dynamics in liquid para-hydrogen at two state points and liquid ortho-deuterium at one state point. The CMD results are compared with the results of classical molecular dynamics, quantum mode coupling theory, a maximum entropy analytic continuation approach, pair-product forward- backward semiclassical dynamics, and available experimental results. The self-diffusion constants are in excellent agreement with the experimental measurements for all systems studied. Furthermore, it is shown that the method is able to adequately describe both the single-particle and collective dynamics of quantum liquids. (c) 2004 American Institute of Physics

A complete catalog of stellar mass maps for PHANGS

NASA Astrophysics Data System (ADS)

Munoz-Mateos, Juan-Carlos; Querejeta, Miguel; Schinnerer, Eva; Leroy, Adam; Sun, Jiayi; Blanc, Guillermo; Kruijssen, Diederik; Emsellem, Eric; Bigiel, Frank

2018-05-01

We request IRAC 3.6 and 4.5 um imaging of four galaxies that have been mapped in molecular gas by ALMA as part of its first large program targeting nearby galaxies (PHANGS: Physics at High Angular resolution in Nearby GalaxieS). IRAC provides a uniquely robust view of the stellar mass distribution, which in turn plays a key role in regulating the properties and behavior of the molecular gas. These are the only targets of our ALMA large program without such imaging. A modest investment of Spitzer time will allow us to measure the drivers of molecular cloud and star formation in these targets.

Concentration Dependent Speciation and Mass Transport Properties of Switchable Polarity Solvents

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

Aaron D. Wilson; Christopher J. Orme

2014-12-01

Tertiary amine switchable polarity solvents (SPS) consisting of predominantly water, tertiary amine, and tertiary ammonium and bicarbonate ions were produced at various concentrations for three different amines: N,N-dimethylcyclohexylamine, N,N-dimethyloctylamine, and 1 cyclohexylpiperidine. For all concentrations, physical properties were measured including viscosity, molecular diffusion coefficients, freezing point depression, and density. Based on these measurements a variation on the Mark Houwink equation was developed to predict the viscosity of any tertiary amine SPS as a function of concentration using the amine’s molecular mass. The observed physical properties allowed the identification of solution state speciation of non-osmotic SPS, where the amine to carbonicmore » acid ratio is significantly greater than one. These results indicate that at most concentrations the stoichiometric excess amine is involved in solvating a proton with two amines. The physical properties of osmotic SPS have consistent concentration dependence behavior over a wide range of concentrations; this consistence suggests osmotic pressures based on low concentrations freezing point studies can be reliably extrapolated to higher concentrations.« less

Transmission of chirality through space and across length scales

NASA Astrophysics Data System (ADS)

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

2017-05-01

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

Effect of zinc oxide on the electronic properties of carbonated hydroxyapatite

NASA Astrophysics Data System (ADS)

Refaat, Ahmed; Youness, Rasha A.; Taha, Mohammed A.; Ibrahim, Medhat

2017-11-01

Zinc oxide (ZnO)-doped carbonate substituted hydroxyapatite (CHA) was successfully prepared with different ZnO contents up to 3 wt% and then samples were subjected to study with Fourier transform infrared (FTIR) spectroscopy. FTIR indicated that the interaction is physical and consequently molecular modeling was consulted to understand the effect of ZnO upon CHA. A model molecule of Ca10(PO4)6(OH)2·14H2O was built then interacted with Zn with different schemes through 4 active sites namely O of (PO4); O of OH; Ca of Ca(OH)2 and P of (PO4). For each interaction, two possibilities were tried; one through oxygen and the other through zinc of ZnO. The interaction of ZnO with CHA resulted in changes in the physical properties such as the final heat of formation, ionization potential, and even molecular dimensions. This may be due to the change in the electronic distribution which in turn changes the total dipole moment and hence the reactivity that could also affect the physical properties.

T.D.S. spectroscopic databank for spherical tops: DOS version

NASA Astrophysics Data System (ADS)

Tyuterev, V. G.; Babikov, Yu. L.; Tashkun, S. A.; Perevalov, V. I.; Nikitin, A.; Champion, J.-P.; Wenger, C.; Pierre, C.; Pierre, G.; Hilico, J.-C.; Loete, M.

1994-10-01

T.D.S. (Traitement de Donnees Spectroscopiques or Tomsk-Dijon-Spectroscopy project) is a computer package concerned with high resolution spectroscopy of spherical top molecules like CH4, CF4, SiH4, SiF4, SnH4, GeH4, SF6, etc. T.D.S. contains information, fundamental spectroscopic data (energies, transition moments, spectroscopic constants) recovered from comprehensive modeling and simultaneous fitting of experimental spectra, and associated software written in C. The T.D.S. goal is to provide an access to all available information on vibration-rotation molecular states and transitions including various spectroscopic processes (Stark, Raman, etc.) under extended conditions based on extrapolations of laboratory measurements using validated theoretical models. Applications for T.D.S. may include: education/training in molecular physics, quantum chemistry, laser physics; spectroscopic applications (analysis, laser spectroscopy, atmospheric optics, optical standards, spectroscopic atlases); applications to environment studies and atmospheric physics (remote sensing); data supply for specific databases; and to photochemistry (laser excitation, multiphoton processes). The reported DOS-version is designed for IBM and compatible personal computers.

Deep, Broadband Spectral Line Surveys of Molecule-rich Interstellar Clouds

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

Widicus Weaver, Susanna L.; Laas, Jacob C.; Zou, Luyao

2017-09-01

Spectral line surveys are an indispensable tool for exploring the physical and chemical evolution of astrophysical environments due to the vast amount of data that can be obtained in a relatively short amount of time. We present deep, broadband spectral line surveys of 30 interstellar clouds using two broadband λ  = 1.3 mm receivers at the Caltech Submillimeter Observatory. This information can be used to probe the influence of physical environment on molecular complexity. We observed a wide variety of sources to examine the relative abundances of organic molecules as they relate to the physical properties of the source (i.e., temperature,more » density, dynamics, etc.). The spectra are highly sensitive, with noise levels ≤25 mK at a velocity resolution of ∼0.35 km s{sup −1}. In the initial analysis presented here, column densities and rotational temperatures have been determined for the molecular species that contribute significantly to the spectral line density in this wavelength regime. We present these results and discuss their implications for complex molecule formation in the interstellar medium.« less

USSR and Eastern Europe Scientific Abstracts, Physics and Mathematics. Number 37.

DTIC Science & Technology

1977-12-07

when the pressure is zero. The magnetic field was created with a Hemlholtz design superconducting magnet with the magnetic field perpendicu- lar to...titanium resonator, the distribution of the magnetic field in the cross section created by the superconducting selonoids and the characteristics of the...Semiconductors 1 Electricity and Magnetism 18 Fluid Dynamics 20 Lasers and Masers 22 Magnetohydrodynamics • 35 Molecular Physics 52 Optics and

Simulation of Quantum Phenomena in Nanowire Sensors

DTIC Science & Technology

2014-12-17

Ag and Pt atoms: search for nanocatalysts, Journal of Physics B: Atomic, Molecular and Optical Physics, (07 2011): 0. doi: 10.1088/0953- 4075/44...International Advisory Committee, African Laser Centre Annual Workshop 3-5 Nov. 2014, Moroccan Foundation for Advanced Science, Innovation & Research...atoms encapsulated inside C180 and C240 we found: 1) The Xe-C180 and Xe-C240 binding energies along some high symmetry directions showed the

Molecular simulation of the thermophysical properties and phase behaviour of impure CO2 relevant to CCS.

PubMed

Cresswell, Alexander J; Wheatley, Richard J; Wilkinson, Richard D; Graham, Richard S

2016-10-20

Impurities from the CCS chain can greatly influence the physical properties of CO 2 . This has important design, safety and cost implications for the compression, transport and storage of CO 2 . There is an urgent need to understand and predict the properties of impure CO 2 to assist with CCS implementation. However, CCS presents demanding modelling requirements. A suitable model must both accurately and robustly predict CO 2 phase behaviour over a wide range of temperatures and pressures, and maintain that predictive power for CO 2 mixtures with numerous, mutually interacting chemical species. A promising technique to address this task is molecular simulation. It offers a molecular approach, with foundations in firmly established physical principles, along with the potential to predict the wide range of physical properties required for CCS. The quality of predictions from molecular simulation depends on accurate force-fields to describe the interactions between CO 2 and other molecules. Unfortunately, there is currently no universally applicable method to obtain force-fields suitable for molecular simulation. In this paper we present two methods of obtaining force-fields: the first being semi-empirical and the second using ab initio quantum-chemical calculations. In the first approach we optimise the impurity force-field against measurements of the phase and pressure-volume behaviour of CO 2 binary mixtures with N 2 , O 2 , Ar and H 2 . A gradient-free optimiser allows us to use the simulation itself as the underlying model. This leads to accurate and robust predictions under conditions relevant to CCS. In the second approach we use quantum-chemical calculations to produce ab initio evaluations of the interactions between CO 2 and relevant impurities, taking N 2 as an exemplar. We use a modest number of these calculations to train a machine-learning algorithm, known as a Gaussian process, to describe these data. The resulting model is then able to accurately predict a much broader set of ab initio force-field calculations at comparatively low numerical cost. Although our method is not yet ready to be implemented in a molecular simulation, we outline the necessary steps here. Such simulations have the potential to deliver first-principles simulation of the thermodynamic properties of impure CO 2 , without fitting to experimental data.

Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose: A Molecular Dynamics Analysis.

PubMed

Smith, Micholas Dean; Cheng, Xiaolin; Petridis, Loukas; Mostofian, Barmak; Smith, Jeremy C

2017-11-03

Deconstruction of cellulose is crucial for the chemical conversion of lignocellulose into fuel/bioproduct precursors. Recently, a water-organosolv cosolvent system (THF-water) has been shown to both phase-separate on cellulose surfaces and partially deconstruct Avicel  (cellulose) in the absence of acid. Here we employ molecular dynamics simulations to determine whether other common water-organosolv cosolvent systems (acetone, ethanol, and γ-valerolactone) exhibit phase separation at cellulose surface and whether this alters a purely physical cellulose dissociation pathway. Despite finding varied degrees of phase-separation of organosolv on cellulose surfaces, physical dissociation is not enhanced. Interestingly, however, the total amount the median water-cellulose contact lifetimes increases for the cosolvent systems in the order of THF > acetone > ethanol > γ-valerolactone. Together our results indicate two points: a purely physical process for deconstruction of cellulose is unlikely for these cosolvents, and in THF-water, unlike γ-valerolactone- (and some concentrations of acetone and ethanol) water cosolvents, a significant fraction of surface water is slowed. This slowing may be of importance in enhancing chemical deconstruction of cellulose, as it permits an increase in potential THF-water-cellulose reactions, even while the amount of water near cellulose is decreased.

Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose: A Molecular Dynamics Analysis

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

Smith, Micholas Dean; Cheng, Xiaolin; Petridis, Loukas

Deconstruction of cellulose is crucial for the chemical conversion of lignocellulose into fuel/bioproduct precursors. Recently, a water-organosolv cosolvent system (THF-water) has been shown to both phase-separate on cellulose surfaces and partially deconstruct Avicel (cellulose) in the absence of acid. Here we employ molecular dynamics simulations to determine whether other common water-organosolv cosolvent systems (acetone, ethanol, and γ-valerolactone) exhibit phase separation at cellulose surface and whether this alters a purely physical cellulose dissociation pathway. Despite finding varied degrees of phase-separation of organosolv on cellulose surfaces, physical dissociation is not enhanced. Interestingly, however, the total amount the median water-cellulose contact lifetimes increasesmore » for the cosolvent systems in the order of THF > acetone > ethanol > γ-valerolactone. Together our results indicate two points: a purely physical process for deconstruction of cellulose is unlikely for these cosolvents, and in THF-water, unlike γ-valerolactone- (and some concentrations of acetone and ethanol) water cosolvents, a significant fraction of surface water is slowed. As a result, this slowing may be of importance in enhancing chemical deconstruction of cellulose, as it permits an increase in potential THF-water-cellulose reactions, even while the amount of water near cellulose is decreased.« less

Modelling human behaviour in a bumper car ride using molecular dynamics tools: a student project

NASA Astrophysics Data System (ADS)

Buendía, Jorge J.; Lopez, Hector; Sanchis, Guillem; Pardo, Luis Carlos

2017-05-01

Amusement parks are excellent laboratories of physics, not only to check physical laws, but also to investigate if those physical laws might also be applied to human behaviour. A group of Physics Engineering students from Universitat Politècnica de Catalunya has investigated if human behaviour, when driving bumper cars, can be modelled using tools borrowed from the analysis of molecular dynamics simulations, such as the radial and angular distribution functions. After acquiring several clips and obtaining the coordinates of the cars, those magnitudes are computed and analysed. Additionally, an analogous hard disks system is simulated to compare its distribution functions to those obtained from the cars’ coordinates. Despite the clear difference between bumper cars and a hard disk-like particle system, the obtained distribution functions are very similar. This suggests that there is no important effect of the individuals in the collective behaviour of the system in terms of structure. The research, performed by the students, has been undertaken in the frame of a motivational project designed to approach the scientific method for university students named FISIDABO. This project offers both the logistical and technical support to undertake the experiments designed by students at the amusement park of Barcelona TIBIDABO and accompanies them all along the scientific process.

Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose: A Molecular Dynamics Analysis

DOE PAGES

Smith, Micholas Dean; Cheng, Xiaolin; Petridis, Loukas; ...

2017-11-03

Deconstruction of cellulose is crucial for the chemical conversion of lignocellulose into fuel/bioproduct precursors. Recently, a water-organosolv cosolvent system (THF-water) has been shown to both phase-separate on cellulose surfaces and partially deconstruct Avicel (cellulose) in the absence of acid. Here we employ molecular dynamics simulations to determine whether other common water-organosolv cosolvent systems (acetone, ethanol, and γ-valerolactone) exhibit phase separation at cellulose surface and whether this alters a purely physical cellulose dissociation pathway. Despite finding varied degrees of phase-separation of organosolv on cellulose surfaces, physical dissociation is not enhanced. Interestingly, however, the total amount the median water-cellulose contact lifetimes increasesmore » for the cosolvent systems in the order of THF > acetone > ethanol > γ-valerolactone. Together our results indicate two points: a purely physical process for deconstruction of cellulose is unlikely for these cosolvents, and in THF-water, unlike γ-valerolactone- (and some concentrations of acetone and ethanol) water cosolvents, a significant fraction of surface water is slowed. As a result, this slowing may be of importance in enhancing chemical deconstruction of cellulose, as it permits an increase in potential THF-water-cellulose reactions, even while the amount of water near cellulose is decreased.« less

Assessment of physical stability of an antibody drug conjugate by higher order structure analysis: impact of thiol- maleimide chemistry.

PubMed

Guo, Jianxin; Kumar, Sandeep; Prashad, Amarnauth; Starkey, Jason; Singh, Satish K

2014-07-01

To provide a systematic biophysical approach towards a better understanding of impact of conjugation chemistry on higher order structure and physical stability of an antibody drug conjugate (ADC). ADC was prepared using thiol-maleimide chemistry. Physical stabilities of ADC and its parent IgG1 mAb were compared using calorimetric, spectroscopic and molecular modeling techniques. ADC and mAb respond differently to thermal stress. Both the melting temperatures and heat capacities are substantially lower for the ADC. Spectroscopic experiments show that ADC and mAb have similar secondary and tertiary structures, but these are more easily destabilized by thermal stress on the ADC indicating reduced conformational stability. Molecular modeling calculations suggest a substantial decrease in the conformational energy of the mAb upon conjugation. The local surface around the conjugation sites also becomes more hydrophobic in the ADC, explaining the lower colloidal stability and greater tendency of the ADC to aggregate. Computational and biophysical analyses of an ADC and its parent mAb have provided insights into impact of conjugation on physical stability and pinpointed reasons behind lower structural stability and increased aggregation propensity of the ADC. This knowledge can be used to design appropriate formulations to stabilize the ADC.

Interactive Molecular Graphics for Augmented Reality Using HoloLens.

PubMed

Müller, Christoph; Krone, Michael; Huber, Markus; Biener, Verena; Herr, Dominik; Koch, Steffen; Reina, Guido; Weiskopf, Daniel; Ertl, Thomas

2018-06-13

Immersive technologies like stereo rendering, virtual reality, or augmented reality (AR) are often used in the field of molecular visualisation. Modern, comparably lightweight and affordable AR headsets like Microsoft's HoloLens open up new possibilities for immersive analytics in molecular visualisation. A crucial factor for a comprehensive analysis of molecular data in AR is the rendering speed. HoloLens, however, has limited hardware capabilities due to requirements like battery life, fanless cooling and weight. Consequently, insights from best practises for powerful desktop hardware may not be transferable. Therefore, we evaluate the capabilities of the HoloLens hardware for modern, GPU-enabled, high-quality rendering methods for the space-filling model commonly used in molecular visualisation. We also assess the scalability for large molecular data sets. Based on the results, we discuss ideas and possibilities for immersive molecular analytics. Besides more obvious benefits like the stereoscopic rendering offered by the device, this specifically includes natural user interfaces that use physical navigation instead of the traditional virtual one. Furthermore, we consider different scenarios for such an immersive system, ranging from educational use to collaborative scenarios.

Development of a Submillimeter Multipass Spectrometer for the Study of Molecular Ions

NASA Astrophysics Data System (ADS)

Carroll, A.; Rocher, B.; Laas, J. C.; Deprince, B. A.; Hays, B.; Weaver, S. L. Widicus; Lang, S.

2012-06-01

We have developed a multipass spectrometer for the submillimeter spectral region that is being used to study molecular ions through gas phase spectroscopy. The optical configuration is based on the design of Perry and coworkers that was implemented in the optical regime. To our knowledge, this is the first implementation of this optical configuration at long wavelengths. The setup involves two nearly concentric spherical mirrors that focus the multiple beam passes into a small area, or ``waist'', in the middle of the sample chamber. A supersonic molecular beam is coupled to the setup so that the molecular beam crosses the optical path at the waist. Initial studies have focused on neutral test molecules to probe the physical properties of the molecular beam under various arrangements of the molecular source relative to the optical path. Current studies focus on coupling a plasma discharge source to the setup to enable the study of molecular ions. Here we present the design of this instrument, compare the spectrometer capabilities to a traditional single pass spectrometer, and discuss the results of initial spectroscopic studies.

The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

NASA Astrophysics Data System (ADS)

Chen, Jundong

2018-03-01

Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

Molecularly thin fluoro-polymeric nanolubricant films: tribology, rheology, morphology, and applications.

PubMed

Chung, Pil Seung; Jhon, Myung S; Choi, Hyoung Jin

2016-03-21

Molecularly thin perfluoropolyether (PFPE) has been used extensively as a high-performance lubricant in various applications and, more importantly, on carbon overcoats to enhance the reliability and lubrication of micro-/nanoelectro-mechanical systems, where the tribological performance caused by its molecular architecture is a critical issue, as are its physical properties and rheological characteristics. This Highlight addresses recent trends in the development of fluoro-polymeric lubricant films with regard to their tribology, rheology, and physio-chemical properties as they relate to heat-assisted magnetic recording. Nanorheology has been employed to examine the dynamic response of nonfunctional and functional PFPEs, while the viscoelastic properties of nanoscale PFPE films and the relaxation processes as a function of molecular structure and end-group functionality were analyzed experimentally; furthermore, the characteristics of binary blends were reported.

Computer-aided design of polymers and composites

NASA Technical Reports Server (NTRS)

Kaelble, D. H.

1985-01-01

This book on computer-aided design of polymers and composites introduces and discusses the subject from the viewpoint of atomic and molecular models. Thus, the origins of stiffness, strength, extensibility, and fracture toughness in composite materials can be analyzed directly in terms of chemical composition and molecular structure. Aspects of polymer composite reliability are considered along with characterization techniques for composite reliability, relations between atomic and molecular properties, computer aided design and manufacture, polymer CAD/CAM models, and composite CAD/CAM models. Attention is given to multiphase structural adhesives, fibrous composite reliability, metal joint reliability, polymer physical states and transitions, chemical quality assurance, processability testing, cure monitoring and management, nondestructive evaluation (NDE), surface NDE, elementary properties, ionic-covalent bonding, molecular analysis, acid-base interactions, the manufacturing science, and peel mechanics.

[Physical methods and molecular biology].

PubMed

Serdiuk, I N

2009-01-01

The review is devoted to the description of the current state of physical and chemical methods used for studying the structural and functional bases of living processes. Special attention is focused on the physical methods that have opened a new page in the research of the structure of biological macromolecules. They include primarily the methods of detecting and manipulating single molecules using optical and magnetic traps. New physical methods, such as two-dimensional infrared spectroscopy, fluorescence correlation spectroscopy and magnetic resonance microscopy are also analyzed briefly in the review. The path that physics and biology have passed for the latest 55 years shows that there is no single method providing all necessary information on macromolecules and their interactions. Each method provides its space-time view of the system. All physical methods are complementary. It is just complementarity that is the fundamental idea justifying the existence in practice of all physical methods, whose description is the aim of the review.

Recent advances in magnetic resonance microscopy to the physical structure characterization of carbonaceous and inorganic materials

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

Gregory, D.M.; Gerald, R.E.; Cody, G.D.

1997-04-01

Magnetic resonance microscopy (MRM) techniques have been employed to study the molecular architectures and properties of structural polymers, fossil fuels, microporous carbons and inorganic catalysts.

Preface

NASA Astrophysics Data System (ADS)

Barnes, Austin J.; Schmitt, Michael

2015-06-01

EUCMOS XXXII, the 32nd European Congress on Molecular Spectroscopy, was held during August 24-29, 2014, at the Heinrich-Heine University, Düsseldorf, Germany. The meeting was organised by the Institute of Physical Chemistry of the Heinrich-Heine University.

PHYSICOCHEMICAL PROPERTY CALCULATIONS

EPA Science Inventory

Computer models have been developed to estimate a wide range of physical-chemical properties from molecular structure. The SPARC modeling system approaches calculations as site specific reactions (pKa, hydrolysis, hydration) and `whole molecule' properties (vapor pressure, boilin...

Stimulated Raman scattering: old physics, new applications.

PubMed

Yakovlev, Vladislav V; Petrov, Georgi I; Zhang, Hao F; Noojin, Gary D; Denton, Michael L; Thomas, Robert J; Scully, Marlan O

2009-10-01

Stimulated Raman scattering as a promising way of expanding the tunability of ultrafast lasers and as an exciting new biomedical imaging modality capable of selective excitation and chemically-specific diagnostics of molecular species.

An open source digital servo for atomic, molecular, and optical physics experiments

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

Leibrandt, D. R., E-mail: david.leibrandt@nist.gov; Heidecker, J.

2015-12-15

We describe a general purpose digital servo optimized for feedback control of lasers in atomic, molecular, and optical physics experiments. The servo is capable of feedback bandwidths up to roughly 1 MHz (limited by the 320 ns total latency); loop filter shapes up to fifth order; multiple-input, multiple-output control; and automatic lock acquisition. The configuration of the servo is controlled via a graphical user interface, which also provides a rudimentary software oscilloscope and tools for measurement of system transfer functions. We illustrate the functionality of the digital servo by describing its use in two example scenarios: frequency control of themore » laser used to probe the narrow clock transition of {sup 27}Al{sup +} in an optical atomic clock, and length control of a cavity used for resonant frequency doubling of a laser.« less

An open source digital servo for atomic, molecular, and optical physics experiments.

PubMed

Leibrandt, D R; Heidecker, J

2015-12-01

We describe a general purpose digital servo optimized for feedback control of lasers in atomic, molecular, and optical physics experiments. The servo is capable of feedback bandwidths up to roughly 1 MHz (limited by the 320 ns total latency); loop filter shapes up to fifth order; multiple-input, multiple-output control; and automatic lock acquisition. The configuration of the servo is controlled via a graphical user interface, which also provides a rudimentary software oscilloscope and tools for measurement of system transfer functions. We illustrate the functionality of the digital servo by describing its use in two example scenarios: frequency control of the laser used to probe the narrow clock transition of (27)Al(+) in an optical atomic clock, and length control of a cavity used for resonant frequency doubling of a laser.

Mechanisms that Underlie Co-variation of the Brain and Face

PubMed Central

Marcucio, Ralph S.; Young, Nathan M.; Hu, Diane; Hallgrimsson, Benedikt

2011-01-01

The effect of the brain on the morphology of the face has long been recognized in both evolutionary biology and clinical medicine. In this paper we describe factors that are active between development of the brain and face and how these might impact craniofacial variation. First, there is the physical influence of the brain, which contributes to overall growth and morphology of the face through direct structural interactions. Second, there is the molecular influence of the brain, which signals to facial tissues to establish signaling centers that regulate patterned growth. Importantly, subtle alterations to these physical or molecular interactions may contribute to both normal and abnormal variation. These interactions are therefore critical to our understanding of how a diversity of facial morphologies can be generated both within species and across evolutionary time. PMID:21381182

Randic and Schultz molecular topological indices and their correlation with some X-ray absorption parameters

NASA Astrophysics Data System (ADS)

Khatri, Sunil; Kekre, Pravin A.; Mishra, Ashutosh

2016-10-01

The properties of a molecular system are affected by the topology of molecule. Therefore many studies have been made where the various physic-chemical properties are correlated with the topological indices. These studies have shown a very good correlation demonstrating the utility of the graph theoretical approach. It is, therefore, very natural to expect that the various physical properties obtained by the X-ray absorption spectra may also show correlation with the topological indices. Some complexes were used to establish correlation between topological indices and some X-ray absorption parameters like chemical shift. The chemical shift is on the higher energy side of the metal edge in these complexes. The result obtained in these studies shows that the topological indices of organic molecule acting as a legands can be used for estimating edge shift theoretically.

Implications of Tumor Heterogeneity for Precision Medicine

NASA Astrophysics Data System (ADS)

Jeraj, Robert

Medical physics is intimately connected with medicine, and is progressing along a similar path. General trend of medicine, particularly oncology, towards personalized treatment gave rise to precision medicine, which addresses the highly complex nature of disease. However, there are severe obstacles to overcome. For example, cancers evolve in time to become harder targets to treat. Understanding treatment resistance, and its development, often connected with the highly heterogeneous nature of the disease, is another key obstacle. Use of multi-modality imaging techniques such as molecular imaging is one of the solutions that medical physics can offer. Examples from clinical trials utilizing advanced molecular imaging, highlighting intra-tumor and inter-tumor heterogeneity will be presented. New understanding of cancer treatment response dynamics will be outlined. Potential for improved patient treatment designs steaming from these novel insights will be discussed.

Nanoarchitectonics

NASA Astrophysics Data System (ADS)

Ariga, Katsuhiko; Aono, Masakazu

2016-11-01

The construction of functional systems with nanosized parts would not possible by simple technology (nanotechnology). It can be handled by certain kinds of more sophisticated carpenter work or artistic architectonics (nanoarchitectonics). However, architecting materials in the nanoscale is not very simple because of various unexpected and uncontrollable thermal/statistical fluctuations and mutual interactions. The latter factors inevitably disturb the interactions between component building blocks. Therefore, several techniques and actions, including the regulation of atomic/molecular manipulation, molecular modification by organic chemistry, control of physicochemical interactions, self-assembly/organization, and application of external physical stimuli, must be well combined. This short review describes the historical backgrounds and essences of nanoarchitectonics, followed by a brief introduction of recent examples related to nanoarchitectonics. These examples are categorized in accordance with their physical usages: (i) atom/molecule control; (ii) devices and sensors; (iii) the other applications based on interfacial nanoarchitectonics.

Behavior dynamics: One perspective

PubMed Central

Marr, M. Jackson

1992-01-01

Behavior dynamics is a field devoted to analytic descriptions of behavior change. A principal source of both models and methods for these descriptions is found in physics. This approach is an extension of a long conceptual association between behavior analysis and physics. A theme common to both is the role of molar versus molecular events in description and prediction. Similarities and differences in how these events are treated are discussed. Two examples are presented that illustrate possible correspondence between mechanical and behavioral systems. The first demonstrates the use of a mechanical model to describe the molar properties of behavior under changing reinforcement conditions. The second, dealing with some features of concurrent schedules, focuses on the possible utility of nonlinear dynamical systems to the description of both molar and molecular behavioral events as the outcome of a deterministic, but chaotic, process. PMID:16812655

Molecular machines operating on the nanoscale: from classical to quantum

PubMed Central

2016-01-01

Summary The main physical features and operating principles of isothermal nanomachines in the microworld, common to both classical and quantum machines, are reviewed. Special attention is paid to the dual, constructive role of dissipation and thermal fluctuations, the fluctuation–dissipation theorem, heat losses and free energy transduction, thermodynamic efficiency, and thermodynamic efficiency at maximum power. Several basic models are considered and discussed to highlight generic physical features. This work examines some common fallacies that continue to plague the literature. In particular, the erroneous beliefs that one should minimize friction and lower the temperature for high performance of Brownian machines, and that the thermodynamic efficiency at maximum power cannot exceed one-half are discussed. The emerging topic of anomalous molecular motors operating subdiffusively but very efficiently in the viscoelastic environment of living cells is also discussed. PMID:27335728

An open source digital servo for atomic, molecular, and optical physics experiments

NASA Astrophysics Data System (ADS)

Leibrandt, D. R.; Heidecker, J.

2015-12-01

We describe a general purpose digital servo optimized for feedback control of lasers in atomic, molecular, and optical physics experiments. The servo is capable of feedback bandwidths up to roughly 1 MHz (limited by the 320 ns total latency); loop filter shapes up to fifth order; multiple-input, multiple-output control; and automatic lock acquisition. The configuration of the servo is controlled via a graphical user interface, which also provides a rudimentary software oscilloscope and tools for measurement of system transfer functions. We illustrate the functionality of the digital servo by describing its use in two example scenarios: frequency control of the laser used to probe the narrow clock transition of 27Al+ in an optical atomic clock, and length control of a cavity used for resonant frequency doubling of a laser.

An open source digital servo for atomic, molecular, and optical physics experiments

PubMed Central

Leibrandt, D. R.; Heidecker, J.

2016-01-01

We describe a general purpose digital servo optimized for feedback control of lasers in atomic, molecular, and optical physics experiments. The servo is capable of feedback bandwidths up to roughly 1 MHz (limited by the 320 ns total latency); loop filter shapes up to fifth order; multiple-input, multiple-output control; and automatic lock acquisition. The configuration of the servo is controlled via a graphical user interface, which also provides a rudimentary software oscilloscope and tools for measurement of system transfer functions. We illustrate the functionality of the digital servo by describing its use in two example scenarios: frequency control of the laser used to probe the narrow clock transition of 27Al+ in an optical atomic clock, and length control of a cavity used for resonant frequency doubling of a laser. PMID:26724014

The Hydra model - a model for what?

PubMed

Gierer, Alfred

2012-01-01

The introductory personal remarks refer to my motivations for choosing research projects, and for moving from physics to molecular biology and then to development, with Hydra as a model system. Historically, Trembley's discovery of Hydra regeneration in 1744 was the beginning of developmental biology as we understand it, with passionate debates about preformation versus de novo generation, mechanisms versus organisms. In fact, seemingly conflicting bottom-up and top-down concepts are both required in combination to understand development. In modern terms, this means analysing the molecules involved, as well as searching for physical principles underlying development within systems of molecules, cells and tissues. During the last decade, molecular biology has provided surprising and impressive evidence that the same types of molecules and molecular systems are involved in pattern formation in a wide range of organisms, including coelenterates like Hydra, and thus appear to have been "invented" early in evolution. Likewise, the features of certain systems, especially those of developmental regulation, are found in many different organisms. This includes the generation of spatial structures by the interplay of self-enhancing activation and "lateral" inhibitory effects of wider range, which is a main topic of my essay. Hydra regeneration is a particularly clear model for the formation of defined patterns within initially near-uniform tissues. In conclusion, this essay emphasizes the analysis of development in terms of physical laws, including the application of mathematics, and insists that Hydra was, and will continue to be, a rewarding model for understanding general features of embryogenesis and regeneration.

The 1999 Conference on Molecular Energy Transfer (COMET XVI)

DTIC Science & Technology

1999-07-14

Farrell,* John D. DeSain, Craig A. Taaties Combustion Research Facility, Mail Stop 9055, Sandia National Laboratories, Livermore, CA 94551-0969 The...Knowles, with contributions by J. Alml~f, R. D. Amos, M. J. 0. Deegan , S. T. Elbert, C. Hampel, W. Meyer, K. A. Peterson, R. M. Pitzer, A. J. Stone...Department of Molecular and Laser Physics Fax: +84 564 54 2254 University of Nijmegen Toernooi veld 1 6525 Nijmegen Taatjes, Craig The Netherlands

Environmentally stable polymers and coatings for space application: CH-5, supplement 10

NASA Technical Reports Server (NTRS)

Sykes, G.

1986-01-01

High molecular weight, randomly coupled poly(imide siloxane) soluble block copolymers were synthesized from bis(amino propyl) polydimethylsiloxane equilibrates of various molecular weights, aromatic metalinked diamines, and 3,3'-4,4'-benzophenone tetracarboxylic dianhydride (BTDA). Two synthetic procedures were successfully used to synthesize the poly(amic acid siloxane) intermediates. For both synthetic procedures, a cosolvent system was employed to achieve complete solvation of all components throughout the polymerization. Physical property characterization is continuing.

Evolutionary Specialization of Tactile Perception in Vertebrates.

PubMed

Schneider, Eve R; Gracheva, Elena O; Bagriantsev, Slav N

2016-05-01

Evolution has endowed vertebrates with the remarkable tactile ability to explore the world through the perception of physical force. Yet the sense of touch remains one of the least well understood senses at the cellular and molecular level. Vertebrates specializing in tactile perception can highlight general principles of mechanotransduction. Here, we review cellular and molecular adaptations that underlie the sense of touch in typical and acutely mechanosensitive vertebrates. ©2016 Int. Union Physiol. Sci./Am. Physiol. Soc.

Chemical and Physical Characterization of the Activation of Ribulosebiphosphate Carboxylase/Oxygenase

DOE R&D Accomplishments Database

Donnelly, M. I.; Ramakrishnan, V.; Hartman, F. C.

1983-08-01

Molecular structure of ribulosebiphosphate carboxylase/oxygenase isolated from Rhodospirillium was compared with the enzyme isolated from Alcaligens eutrophus. Peptides derived from the active center of the bacterial enzyme were highly homologous with those isolated from spinach. Molecular shapes of the carboxylases were estimated using neutron scattering data. These studies suggested that the enzyme as isolated from R. rubrum is a solid prolate ellipsoid or cylinder, while the spinach enzyme resembles a hollow sphere.

Multiscale equation-free algorithms for molecular dynamics

NASA Astrophysics Data System (ADS)

Abi Mansour, Andrew

Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.

Regulation of circadian blood pressure: from mice to astronauts.

PubMed

Agarwal, Rajiv

2010-01-01

Circadian variation is commonly seen in healthy people; aberration in these biological rhythms is an early sign of disease. Impaired circadian variation of blood pressure (BP) has been shown to be associated with greater target organ damage and with an elevated risk of cardiovascular events independent of the BP load. The purpose of this review is to examine the physiology of circadian BP variation and propose a tripartite model that explains the regulation of circadian BP. The time-keeper in mammals resides centrally in the suprachiasmatic nucleus. Apart from this central clock, molecular clocks exist in most peripheral tissues including vascular tissue and the kidney. These molecular clocks regulate sodium balance, sympathetic function and vascular tone. A physiological model is proposed that integrates our understanding of molecular clocks in mice with the circadian BP variation among humans. The master regulator in this proposed model is the sleep-activity cycle. The equivalents of peripheral clocks are endothelial and adrenergic functions. Thus, in the proposed model, the variation in circadian BP is dependent upon three major factors: physical activity, autonomic function, and sodium sensitivity. The integrated consideration of physical activity, autonomic function, and sodium sensitivity appears to explain the physiology of circadian BP variation and the pathophysiology of disrupted BP rhythms in various conditions and disease states. Our understanding of molecular clocks in mice may help to explain the provenance of blunted circadian BP variation even among astronauts.

Membrane re-modelling by BAR domain superfamily proteins via molecular and non-molecular factors.

PubMed

Nishimura, Tamako; Morone, Nobuhiro; Suetsugu, Shiro

2018-04-17

Lipid membranes are structural components of cell surfaces and intracellular organelles. Alterations in lipid membrane shape are accompanied by numerous cellular functions, including endocytosis, intracellular transport, and cell migration. Proteins containing Bin-Amphiphysin-Rvs (BAR) domains (BAR proteins) are unique, because their structures correspond to the membrane curvature, that is, the shape of the lipid membrane. BAR proteins present at high concentration determine the shape of the membrane, because BAR domain oligomers function as scaffolds that mould the membrane. BAR proteins co-operate with various molecular and non-molecular factors. The molecular factors include cytoskeletal proteins such as the regulators of actin filaments and the membrane scission protein dynamin. Lipid composition, including saturated or unsaturated fatty acid tails of phospholipids, also affects the ability of BAR proteins to mould the membrane. Non-molecular factors include the external physical forces applied to the membrane, such as tension and friction. In this mini-review, we will discuss how the BAR proteins orchestrate membrane dynamics together with various molecular and non-molecular factors. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Molecular gearing systems

DOE PAGES

Gakh, Andrei A.; Sachleben, Richard A.; Bryan, Jeff C.

1997-11-01

The race to create smaller devices is fueling much of the research in electronics. The competition has intensified with the advent of microelectromechanical systems (MEMS), in which miniaturization is already reaching the dimensional limits imposed by physics of current lithographic techniques. Also, in the realm of biochemistry, evidence is accumulating that certain enzyme complexes are capable of very sophisticated modes of motion. Complex synergistic biochemical complexes driven by sophisticated biomechanical processes are quite common. Their biochemical functions are based on the interplay of mechanical and chemical processes, including allosteric effects. In addition, the complexity of this interplay far exceeds thatmore » of typical chemical reactions. Understanding the behavior of artificial molecular devices as well as complex natural molecular biomechanical systems is difficult. Fortunately, the problem can be successfully resolved by direct molecular engineering of simple molecular systems that can mimic desired mechanical or electronic devices. These molecular systems are called technomimetics (the name is derived, by analogy, from biomimetics). Several classes of molecular systems that can mimic mechanical, electronic, or other features of macroscopic devices have been successfully synthesized by conventional chemical methods during the past two decades. In this article we discuss only one class of such model devices: molecular gearing systems.« less

Discovery of a Molecular Collision Front in Interacting Galaxies NGC 4567/4568 with ALMA

NASA Astrophysics Data System (ADS)

Kaneko, Hiroyuki; Kuno, Nario; Saitoh, Takayuki R.

2018-06-01

We present results of 12CO(J = 1–0) imaging observations of NGC 4567/4568, a galaxy pair in a close encounter, with the Atacama Large Millimeter/Submillimeter Array (ALMA). For the first time, we find clear evidence of a molecular collision front with a velocity dispersion that is 16.8 ± 1.4 km s‑1 at the overlapping region, owing to high spatial and velocity resolution. By integrating over the velocity width that corresponds to the molecular collision front, we find a long filamentary structure with a size of 1800 pc × 350 pc at the collision front. This filamentary molecular structure spatially coincides with a dark lane seen in the R-band image. We find four molecular clouds in the filament, each with a radius of 30 pc and mass of 106 M ⊙ the radii matching a typical value for giant molecular clouds (GMCs) and the masses corresponding to those between GMCs and giant molecular associations (GMAs). All four clouds are gravitationally bound. The molecular filamentary structure and its physical conditions are similar to the structure expected via numerical simulation. The filament could be a progenitor of super star clusters.

Physics at the FQMT'11 conference

NASA Astrophysics Data System (ADS)

Špička, V.; Nieuwenhuizen, Th M.; Keefe, P. D.

2012-11-01

This paper deals with the recent state of the art of the following topics presented at the FQMT'11 conference: foundations of quantum physics, quantum measurement; nonequilibrium quantum statistical physics; quantum thermodynamics; quantum measurement, entanglement and coherence; dissipation, dephasing, noise, and decoherence; quantum optics; macroscopic quantum behavior; e.g. cold atoms; Bose-Einstein condensates; physics of quantum computing and quantum information; mesoscopic, nano-electro-mechanical systems and nano-optical systems; spin systems and their dynamics; biological systems and molecular motors; and cosmology, gravitation and astrophysics. The lectures and discussions at the FQMT'11 conference, as well as the contributions to the related topical issue, reveal important themes for future development. The recent literature is included.

Time-dependent compressibility of poly (methyl methacrylate) (PMMA) : an experimental and molecular dynamics investigation

NASA Astrophysics Data System (ADS)

Sane, Sandeep Bhalchandra

This thesis contains three chapters, which describe different aspects of an investigation of the bulk response of Poly(Methyl Methacrylate) (PMMA). The first chapter describes the physical measurements by means of a Belcher/McKinney-type apparatus. Used earlier for the measurement of the bulk response of Poly(Vinyl Acetate), it was now adapted for making measurements at higher temperatures commensurate with the glass transition temperature of PMMA. The dynamic bulk compliance of PMMA was measured at atmospheric pressure over a wide range of temperatures and frequencies, from which the master curves for the bulk compliance were generated by means of the time-temperature superposition principle. It was found that the extent of the transition ranges for the bulk and shear response were comparable. Comparison of the shift factors for bulk and shear responses supports the idea that different molecular mechanisms contribute to shear and bulk deformations. The second chapter delineates molecular dynamics computations for the bulk response for a range of pressures and temperatures. The model(s) consisted of 2256 atoms formed into three polymer chains with fifty monomer units per chain per unit cell. The time scales accessed were limited to tens of pico seconds. It was found that, in addition to the typical energy minimization and temperature annealing cycles for establishing equilibrium models, it is advantageous to subject the model samples to a cycle of relatively large pressures (GPa-range) for improving the equilibrium state. On comparing the computations with the experimentally determined "glassy" behavior, one finds that, although the computations were limited to small samples in a physical sense, the primary limitation rests in the very short times (pico seconds). The molecular dynamics computations do not model the physically observed temperature sensitivity of PMMA, even if one employs a hypothetical time-temperature shift to account for the large difference in time scales between experiment and computation. The values computed by the molecular dynamics method do agree with the values measured at the coldest temperature and at the highest frequency of one kiloHertz. The third chapter draws on measurements of uniaxial, shear and Poisson response conducted previously in our laboratory. With the availability of four time or frequency-dependent material functions for the same material, the process of interconversion between different material functions was investigated. Computed material functions were evaluated against the direct experimental measurements and the limitations imposed on successful interconversion due to the experimental errors in the underlying physical data were explored. Differences were observed that are larger than the experimental errors would suggest.

Deconstructing (and reconstructing) cell migration.

PubMed

Maheshwari, G; Lauffenburger, D A

1998-12-01

An overriding objective in cell biology is to be able to relate properties of particular molecular components to cell behavioral functions and even physiology. In the "traditional" mode of molecular cell biology, this objective has been tackled on a molecule-by-molecule basis, and in the "future" mode sometimes termed "functional genomics," it might be attacked in a high-throughput, parallel manner. Regardless of the manner of approach, the relationship between molecular-level properties and cell-level function is exceedingly difficult to elucidate because of the large number of relevant components involved, their high degree of interconnectedness, and the inescapable fact that they operate as physico-chemical entities-according to the laws of kinetics and mechanics-in space and time within the cell. Cell migration is a prominent representative example of such a cell behavioral function that requires increased understanding for both scientific and technological advance. This article presents a framework, derived from an engineering perspective regarding complex systems, intended to aid in developing improved understanding of how properties of molecular components influence the function of cell migration. That is, cell population migration behavior can be deconstructed as follows: first in terms of a mathematical model comprising cell population parameters (random motility, chemotaxis/haptotaxis, and chemokinesis/haptokinesis coefficients), which in turn depend on characteristics of individual cell paths that can be analyzed in terms of a mathematical model comprising individual cell parameters (translocation speed, directional persistence time, chemotactic/haptotactic index), which in turn depend on cell-level physical processes underlying motility (membrane extension and retraction, cell/substratum adhesion, cell contractile force, front-vs.-rear asymmetry), which in turn depend on molecular-level properties of the plethora of components involved in governance and regulation of these processes. Hence, the influence of any molecular component on cell population migration can be understood by reconstructing these relationships from the molecular level to the physical process level to the individual cell path level to the cell population distribution level. This approach requires combining experimental, theoretical, and computational methodologies from molecular biology, biochemistry, biophysics, and bioengineering.

Self-Consistent-Field Calculation on Lithium Hydride for Undergraduates.

ERIC Educational Resources Information Center

Rioux, Frank; Harriss, Donald K.

1980-01-01

Describes a self-consistent-field-linear combination of atomic orbitals-molecular orbital calculation on the valence electrons of lithium hydride using the method of Roothaan. This description is intended for undergraduate physics students.

Gas-Phase Infrared; JCAMP Format

National Institute of Standards and Technology Data Gateway

SRD 35 NIST/EPA Gas-Phase Infrared; JCAMP Format (PC database for purchase)   This data collection contains 5,228 infrared spectra in the JCAMP-DX (Joint Committee for Atomic and Molecular Physical Data "Data Exchange") format.

Physics in Plastics Technology.

ERIC Educational Resources Information Center

Thomas, Ken

1980-01-01

Discusses the increasing role of the physicist in plastics technology. Relationships of molecular structure to material behavior, design which is related to the material, and the practical problems of fabricating a material into an article are included. (HM)

Yuan T. Lee and Molecular Beam Studies

Science.gov Websites

&D Nuggets Database dropdown arrow Search Tag Cloud Browse Reports Database Help Finding Aids : The Influence of Yuan T. Lee, Journal of Chemical Physics, Volume 125, Issue 13, pp. 132302-132302-19

The 'right' size in nanobiotechnology.

PubMed

Whitesides, George M

2003-10-01

The biological and physical sciences share a common interest in small structures (the definition of 'small' depends on the application, but can range from 1 nm to 1 mm). A vigorous trade across the borders of these areas of science is developing around new materials and tools (largely from the physical sciences) and new phenomena (largely from the biological sciences). The physical sciences offer tools for synthesis and fabrication of devices for measuring the characteristics of cells and sub-cellular components, and of materials useful in cell and molecular biology; biology offers a window into the most sophisticated collection of functional nanostructures that exists.

A bridge from physics to biology.

PubMed

Preparata, Giuliano

2010-01-01

Through molecular biology, the 'atomistic paradigm' tries to remove from the analysis of living matter every element of what appears as the distinguishing character of the chain of the biological processes: their cooperative, collective aspects. Living matter appears, on the contrary, governed by Quantum Field Theory (QFT), spontaneously creating order when the thermodynamical conditions are right. 'Electrodynamical coherence' (EC) is the most promising hint for the existence of a bridge between Physics and Biology.

A Group Contribution Method for Estimating Cetane and Octane Numbers

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

Kubic, William Louis

Much of the research on advanced biofuels is devoted to the study of novel chemical pathways for converting nonfood biomass into liquid fuels that can be blended with existing transportation fuels. Many compounds under consideration are not found in the existing fuel supplies. Often, the physical properties needed to assess the viability of a potential biofuel are not available. The only reliable information available may be the molecular structure. Group contribution methods for estimating physical properties from molecular structure have been used for more than 60 years. The most common application is estimation of thermodynamic properties. More recently, group contributionmore » methods have been developed for estimating rate dependent properties including cetane and octane numbers. Often, published group contribution methods are limited in terms of types of function groups and range of applicability. In this study, a new, broadly-applicable group contribution method based on an artificial neural network was developed to estimate cetane number research octane number, and motor octane numbers of hydrocarbons and oxygenated hydrocarbons. The new method is more accurate over a greater range molecular weights and structural complexity than existing group contribution methods for estimating cetane and octane numbers.« less

Fast surface-based travel depth estimation algorithm for macromolecule surface shape description.

PubMed

Giard, Joachim; Alface, Patrice Rondao; Gala, Jean-Luc; Macq, Benoît

2011-01-01

Travel Depth, introduced by Coleman and Sharp in 2006, is a physical interpretation of molecular depth, a term frequently used to describe the shape of a molecular active site or binding site. Travel Depth can be seen as the physical distance a solvent molecule would have to travel from a point of the surface, i.e., the Solvent-Excluded Surface (SES), to its convex hull. Existing algorithms providing an estimation of the Travel Depth are based on a regular sampling of the molecule volume and the use of the Dijkstra's shortest path algorithm. Since Travel Depth is only defined on the molecular surface, this volume-based approach is characterized by a large computational complexity due to the processing of unnecessary samples lying inside or outside the molecule. In this paper, we propose a surface-based approach that restricts the processing to data defined on the SES. This algorithm significantly reduces the complexity of Travel Depth estimation and makes possible the analysis of large macromolecule surface shape description with high resolution. Experimental results show that compared to existing methods, the proposed algorithm achieves accurate estimations with considerably reduced processing times.

Molecular gas in high-mass filament WB673

NASA Astrophysics Data System (ADS)

Kirsanova, Maria S.; Salii, Svetlana V.; Sobolev, Andrej M.; Olofsson, Anders Olof Henrik; Ladeyschikov, Dmitry A.; Thomasson, Magnus

2017-12-01

We studied the distribution of dense gas in a filamentary molecular cloud containing several dense clumps. The center of the filament is given by the dense clump WB673. The clumps are high-mass and intermediate-mass starforming regions. We observed CS (2-1), 13CO (1-0), C18O(1-0), and methanol lines at 96 GHz toward WB673 with the Onsala Space Observatory 20-m telescope. We found CS (2-1) emission in the inter-clump medium so the clumps are physically connected and the whole cloud is indeed a filament. Its total mass is 104 M⊙ and mass-to-length ratio is 360M⊙ pc-1 from 13CO (1-0) data. Mass-to-length ratio for the dense gas is 3.4 - 34M⊙ pc-1 from CS (2-1) data. The PV-diagram of the filament is V-shaped. We estimated physical conditions in the molecular gas using methanol lines. Location of the filament on the sky between extended shells suggests that it could be a good example to test theoretical models of formation of the filaments via multiple compression of interstellar gas by supersonic waves.

First-Principles Molecular Dynamics Simulations of NaCl in Water: Performance of Advanced Exchange-Correlation Approximations in Density Functional Theory

NASA Astrophysics Data System (ADS)

Yao, Yi; Kanai, Yosuke

Our ability to correctly model the association of oppositely charged ions in water is fundamental in physical chemistry and essential to various technological and biological applications of molecular dynamics (MD) simulations. MD simulations using classical force fields often show strong clustering of NaCl in the aqueous ionic solutions as a consequence of a deep contact pair minimum in the potential of mean force (PMF) curve. First-Principles Molecular Dynamics (FPMD) based on Density functional theory (DFT) with the popular PBE exchange-correlation approximation, on the other hand, show a different result with a shallow contact pair minimum in the PMF. We employed two of most promising exchange-correlation approximations, ωB97xv by Mardiorossian and Head-Gordon and SCAN by Sun, Ruzsinszky and Perdew, to examine the PMF using FPMD simulations. ωB97xv is highly empirically and optimized in the space of range-separated hybrid functional with a dispersion correction while SCAN is the most recent meta-GGA functional that is constructed by satisfying various known conditions in well-defined physical limits. We will discuss our findings for PMF, charge transfer, water dipoles, etc.

What the cognitive neurosciences mean to me.

PubMed

Pereira, Alfredo

2007-01-01

Cognitive Neuroscience is an interdisciplinary area of research that combines measurement of brain activity (mostly by means of neuroimaging) with a simultaneous performance of cognitive tasks by human subjects. These investigations have been successful in the task of connecting the sciences of the brain (Neurosciences) and the sciences of the mind (Cognitive Sciences). Advances on this kind of research provide a map of localization of cognitive functions in the human brain. Do these results help us to understand how mind relates to the brain? In my view, the results obtained by the Cognitive Neurosciences lead to new investigations in the domain of Molecular Neurobiology, aimed at discovering biophysical mechanisms that generate the activity measured by neuroimaging instruments. In this context, I argue that the understanding of how ionic/molecular processes support cognition and consciousness cannot be made by means of the standard reductionist explanations. Knowledge of ionic/molecular mechanisms can contribute to our understanding of the human mind as long as we assume an alternative form of explanation, based on psycho-physical similarities, together with an ontological view of mentality and spirituality as embedded in physical nature (and not outside nature, as frequently assumed in western culture).

What The Cognitive Neurosciences Mean To Me

PubMed Central

Pereira, Alfredo

2007-01-01

Cognitive Neuroscience is an interdisciplinary area of research that combines measurement of brain activity (mostly by means of neuroimaging) with a simultaneous performance of cognitive tasks by human subjects. These investigations have been successful in the task of connecting the sciences of the brain (Neurosciences) and the sciences of the mind (Cognitive Sciences). Advances on this kind of research provide a map of localization of cognitive functions in the human brain. Do these results help us to understand how mind relates to the brain? In my view, the results obtained by the Cognitive Neurosciences lead to new investigations in the domain of Molecular Neurobiology, aimed at discovering biophysical mechanisms that generate the activity measured by neuroimaging instruments. In this context, I argue that the understanding of how ionic/molecular processes support cognition and consciousness cannot be made by means of the standard reductionist explanations. Knowledge of ionic/molecular mechanisms can contribute to our understanding of the human mind as long as we assume an alternative form of explanation, based on psycho-physical similarities, together with an ontological view of mentality and spirituality as embedded in physical nature (and not outside nature, as frequently assumed in western culture). PMID:22058629

Hormesis does not make sense except in the light of TOR-driven aging

PubMed Central

Blagosklonny, Mikhail V.

2011-01-01

Weak stresses (including weak oxidative stress, cytostatic agents, heat shock, hypoxia, calorie restriction) may extend lifespan. Known as hormesis, this is the most controversial notion in gerontology. For one, it is believed that aging is caused by accumulation of molecular damage. If so, hormetic stresses (by causing damage) must shorten lifespan. To solve the paradox, it was suggested that, by activating repair, hormetic stresses eventually decrease damage. Similarly, Baron Munchausen escaped from a swamp by pulling himself up by his own hair. Instead, I discuss that aging is not caused by accumulation of molecular damage. Although molecular damage accumulates, organisms do not live long enough to age from this accumulation. Instead, aging is driven by overactivated signal-transduction pathways including the TOR (Target of Rapamycin) pathway. A diverse group of hormetic conditions can be divided into two groups. “Hormesis A” inhibits the TOR pathway. “Hormesis B” increases aging-tolerance, defined as the ability to survive catastrophic complications of aging. Hormesis A includes calorie restriction, resveratrol, rapamycin, p53-inducing agents and, in part, physical exercise, heat shock and hypoxia. Hormesis B includes ischemic preconditioning and, in part, physical exercise, heat shock, hypoxia and medical interventions. PMID:22166724

Herschel and the Molecular Universe

NASA Technical Reports Server (NTRS)

Tielens, A. G. G. M.; Helmich, F. P.

2006-01-01

Over the next decade, space-based missions will open up the universe to high spatial and spectral resolution studies at infrared and submillimeter wavelengths. This will allow us to study, in much greater detail, the composition and the origin and evolution of molecules in space. Moreover, molecular transitions in these spectral ranges provide a sensitive probe of the dynamics and the physical and chemical conditions in a wide range of objects at scales ranging from budding planetary systems to galactic and extragalactic sizes. Hence, these missions provide us with the tools to study key astrophysical and astrochemical processes involved in the formation and evolution of planets, stars, and galaxies. These new missions can be expected to lead to the detection of many thousands of new spectral features. Identification, analysis and interpretation of these features in terms of the physical and chemical characteristics of the astronomical sources will require detailed astronomical modeling tools supported by laboratory measurements and theoretical studies of chemical reactions and collisional excitation rates on species of astrophysical relevance. These data will have to be made easily accessible to the scientific community through web-based data archives. In this paper, we will review the Herschel mission and its expected impact on our understanding of the molecular universe.

Development of ultralow energy (1–10 eV) ion scattering spectrometry coupled with reflection absorption infrared spectroscopy and temperature programmed desorption for the investigation of molecular solids

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

Bag, Soumabha; Bhuin, Radha Gobinda; Methikkalam, Rabin Rajan J.

2014-01-15

Extremely surface specific information, limited to the first atomic layer of molecular surfaces, is essential to understand the chemistry and physics in upper atmospheric and interstellar environments. Ultra low energy ion scattering in the 1–10 eV window with mass selected ions can reveal extremely surface specific information which when coupled with reflection absorption infrared (RAIR) and temperature programmed desorption (TPD) spectroscopies, diverse chemical and physical properties of molecular species at surfaces could be derived. These experiments have to be performed at cryogenic temperatures and at ultra high vacuum conditions without the possibility of collisions of neutrals and background deposition inmore » view of the poor ion intensities and consequent need for longer exposure times. Here we combine a highly optimized low energy ion optical system designed for such studies coupled with RAIR and TPD and its initial characterization. Despite the ultralow collision energies and long ion path lengths employed, the ion intensities at 1 eV have been significant to collect a scattered ion spectrum of 1000 counts/s for mass selected CH{sub 2}{sup +}.« less

Thermophysical Properties of Energetic Ionic Liquids/Nitric Acid Mixtures: Insights from Molecular Dynamics Simulations

DTIC Science & Technology

2013-01-01

W L. Physical properties of concentrated nitric acid . UNT Digital Library. http://digital.library.unt.edu/ark:/67531/metadc56640/.) 23 M. Engelmann... Nitric Acid Mixtures: Insights from Molecular Dynamics Simulations 5a. CONTRACT NUMBER FA9300-11-C-3012 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER...Rev. 8-98) Prescribed by ANSI Std. 239.18 1     Thermophysical  Properties  of  Energetic  Ionic  Liquids/ Nitric   Acid

Selective and reusable iron(II)-based molecular sensor for the vapor-phase detection of alcohols.

PubMed

Naik, Anil D; Robeyns, Koen; Meunier, Christophe F; Léonard, Alexandre F; Rotaru, Aurelian; Tinant, Bernard; Filinchuk, Yaroslav; Su, Bao Lian; Garcia, Yann

2014-02-03

A mononuclear iron(II) neutral complex (1) is screened for sensing abilities for a wide spectrum of chemicals and to evaluate the response function toward physical perturbation like temperature and mechanical stress. Interestingly, 1 precisely detects methanol among an alcohol series. The sensing process is visually detectable, fatigue-resistant, highly selective, and reusable. The sensing ability is attributed to molecular sieving and subsequent spin-state change of iron centers, after a crystal-to-crystal transformation.

Bohm's Quantum Potential and the Visualization of Molecular Structure

NASA Technical Reports Server (NTRS)

Levit, Creon; Chancellor, Marisa K. (Technical Monitor)

1997-01-01

David Bohm's ontological interpretation of quantum theory can shed light on otherwise counter-intuitive quantum mechanical phenomena including chemical bonding. In the field of quantum chemistry, Richard Bader has shown that the topology of the Laplacian of the electronic charge density characterizes many features of molecular structure and reactivity. Visual and computational examination suggests that the Laplacian of Bader and the quantum potential of Bohm are morphologically equivalent. It appears that Bohmian mechanics and the quantum potential can make chemistry as clear as they makes physics.

Computer Code for Interpreting 13C NMR Relaxation Measurements with Specific Models of Molecular Motion: The Rigid Isotropic and Symmetric Top Rotor Models and the Flexible Symmetric Top Rotor Model

DTIC Science & Technology

2017-01-01

unlimited. 13. SUPPLEMENTARY NOTES 14. ABSTRACT: Carbon-13 nuclear magnetic resonance (13C NMR) spectroscopy is a powerful technique for...FLEXIBLE SYMMETRIC TOP ROTOR MODEL 1. INTRODUCTION Nuclear magnetic resonance (NMR) spectroscopy is a tremendously powerful technique for...application of NMR spectroscopy concerns the property of molecular motion, which is related to many physical, and even biological, functions of molecules in

Infrared Extinction and the Initial Conditions For Star and Planet Formation

NASA Technical Reports Server (NTRS)

Lada, Charles J.

2003-01-01

This grant funds a research program to use infrared extinction measurements to probe the detailed structure of dark molecular clouds and investigate the physical conditions which give rise to star and planet formation. The goals of the this program are to: 1) acquire deep infrared and molecular-line observations of a carefully selected sample of nearby dark clouds, 2) reduce and analyze the data obtained in order to produce detailed extinction maps of the clouds, 3) prepare results, where appropriate, for publication.

High-temperature annealing of graphite: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Petersen, Andrew; Gillette, Victor

2018-05-01

A modified AIREBO potential was developed to simulate the effects of thermal annealing on the structure and physical properties of damaged graphite. AIREBO parameter modifications were made to reproduce Density Functional Theory interstitial results. These changes to the potential resulted in high-temperature annealing of the model, as measured by stored-energy reduction. These results show some resemblance to experimental high-temperature annealing results, and show promise that annealing effects in graphite are accessible with molecular dynamics and reactive potentials.

Coupling of lipid membrane elasticity and in-plane dynamics

NASA Astrophysics Data System (ADS)

Tsang, Kuan-Yu; Lai, Yei-Chen; Chiang, Yun-Wei; Chen, Yi-Fan

2017-07-01

Biomembranes exhibit liquid and solid features concomitantly with their in-plane fluidity and elasticity tightly regulated by cells. Here, we present experimental evidence supporting the existence of the dynamics-elasticity correlations for lipid membranes and propose a mechanism involving molecular packing densities to explain them. This paper thereby unifies, at the molecular level, the aspects of the continuum mechanics long used to model the two membrane features. This ultimately may elucidate the universal physical principles governing the cellular phenomena involving biomembranes.

A 1-D Model of the 4 Bed Molecular Sieve of the Carbon Dioxide Removal Assembly

NASA Technical Reports Server (NTRS)

Coker, Robert; Knox, Jim

2015-01-01

Developments to improve system efficiency and reliability for water and carbon dioxide separation systems on crewed vehicles combine sub-scale systems testing and multi-physics simulations. This paper describes the development of COMSOL simulations in support of the Life Support Systems (LSS) project within NASA's Advanced Exploration Systems (AES) program. Specifically, we model the 4 Bed Molecular Sieve (4BMS) of the Carbon Dioxide Removal Assembly (CDRA) operating on the International Space Station (ISS).

Investigation of uranium molecular species using laser ablation

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

Curreli, Davide

2017-07-12

The goal of this project is to investigate the dynamic evolution of uranium oxide (UOx) molecular species in a rapidly cooling low-temperature plasma using a coupled experimental and modeling approach. Our purpose is to develop quantitative constraints on the UOx phase chemistry under physical conditions similar to that of a nuclear fireball at the time of debris condensation. This work is motivated by a need to better understand the factors controlling uranium chemical fractionation in post-detonation nuclear debris.

Infrared Extinction and the Initial Conditions for Star and Planet Formation

NASA Technical Reports Server (NTRS)

Lada, Charles J.

2002-01-01

This grant funds a research program to use infrared extinction measurements to probe the detailed structure of dark molecular clouds and investigate the physical conditions which give rise to star and planet formation. The goals of the this program are to: (1) acquire deep infrared and molecular-line observations of a carefully selected sample of nearby dark clouds; (2) reduce and analyze the data obtained in order to produce detailed extinction maps of the clouds; and (3) prepare results, where appropriate, for publication.

Photo-control of nanointeractions.

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

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

2005-02-01

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