Using arbitrary trial distributions to improve intramolecular sampling in configurational-bias Monte Carlo

A new formulation of configurational-bias Monte Carlo that uses arbitrary distributions to generate trial bond lengths, angles and dihedrals is described and shown to provide similar acceptance rates with substantially less computational effort. Several different trial distributions are studied and a linear combination of the ideal distribution plus Gaussian distributions automatically fit to the energetic and ideal terms is found to give the best results. The use of these arbitrary trial distributions enables a new formulation of coupled–decoupled configurational bias Monte Carlo that has significantly higher acceptance rates for cyclic molecules. The chemical potential measured via a modified Widom insertion is found to be ill-defined in the case of a molecule that has flexible bond lengths due to the unbounded probability distribution that describes the distance between any two atoms. We propose a simple standard state that allows the computation of consistent chemical potentials for molecules with flexible bonds. We show that the chemical potential via Widom insertion is not computed properly for molecules with Coulombic interactions when the number of trials for any of the nonbonded selection steps is greater than one. Finally, we demonstrate the power of the new algorithms by sampling the side-chain conformations of a polypeptide.     

Six-body van der Waals interactions

We report on the six-body van der Waals interactions within Rydberg atoms. Specifically, we focus on the octahedron case. The results are compared with previous calculations for two to five bodies' interactions. This research is useful for crystal structure in condensed matter physics, such as p-type doping in Silicon or other types of semiconductors. This research is also useful for studying big molecules in chemistry, chemical engineering, and other fields.     

Existence of enantiomeric phase separation in a three-dimensional lattice gas model

A three-dimensional lattice gas model for enantiomeric phase separation is introduced. The enantiomeric molecules (d andl) are the two nonsuperimposable mirror images having the molecular structure C(AB)₂, where C is a tetrahedrally bonded carbon atom with one bond to each end of two AB groups. The lattice gas model consists of a body-centered cubic lattice, each site of which can be either vacant or occupied by a molecule oriented so that the A and B groups point toward neighboring lattice sites. Pairs of molecules interact with short-range, orientationally-dependent interactions. For a domain of interaction parameters, the Pirogov-Sinai extension of the Peierls argument is used to prove thatd-rich andl-rich phases exist in the model at sufficiently low temperature. For another domain of interaction parameters, at sufficiently high chemical potential there is an infinite number of ground states, each containing a racemic mixture ofd andl molecules.     

Aggregates of amphiphilic molecules in lyotropic liquid crystals

Summary Aamphiphilic molecules are made of two parts with different chemical affinities. They build interfaces which limit the contact between these two parts. We shall focus our attention on the case of soap molecules in the presence of water, in which the interfaces separate the paraffinic chains from the water and delimit aggregates of various shapes. Classically the aggregates can be infinite, with flat or cylindrical interfacial curvatures, and packed with long-range translational order in the well-known lamellar, cubic and hexagonal phases; or they can be finite, quasi-spherical and packed without any long-range order in the micellar phase. However, recent investigations show that a long-range ordering of finite aggregates is possible. There is one example of translational order, in which the micelles build a cubic structure, and much more examples now of orientational order. In the latter case the micelles, oblate or prolate spheroids, are dispersed in the solution with their axes nearly parallel to each other, a nematic phase is formed. We shall discuss the possible factors controlling the shapes of the aggregates and their interactions. Laboratoire associé au CNRS (LA No. 2).     

Thermodynamics and kinetics of adsorption of atoms and molecules by carbon nanotubes

Thermodynamics and kinetics of adsorption of atoms and molecules by carbon nanotubes are investigated. Expressions are derived that can be used to perform calculations taking into account various external factors and interactions and, therefore, analyze both physical and chemical adsorption processes and determine its thermodynamic parameters. A mathematical model is developed that makes it possible to find parameters of desorption kinetics separately for molecules adsorbed at different locations and reduce possible systematic errors in analysis of experimental results. Theoretical models are validated by analyzing physical and chemical adsorption of hydrogen and physical adsorption of oxygen.     

The role of the electrostatic interaction in shifting the vibrational frequencies for two adsorbed molecules

We use a simple model to compute the shift of the vibrational frequencies of two adsorbed molecules as a function of inter-molecular distance, and various molecular and metal parameters. We assume that the atoms posses static and dynamic charges and the molecule has an electronic polarizability. The chemical bonds are described by Morse potentials. The electrostatic interactions are computed by a density functional method. We conclude that the use of vibrating point dipoles and of the image theorem in such calculations is an oversimplification.     

Observation of Feshbach-like resonances in collisions between ultracold molecules

We observe magnetically tuned collision resonances for ultracold Cs2 molecules stored in a CO2-laser trap. By magnetically levitating the molecules against gravity, we precisely measure their magnetic moment. We find an avoided level crossing which allows us to transfer the molecules into another state. In the new state, two Feshbach-like collision resonances show up as strong inelastic loss features. We interpret these resonances as being induced by Cs4 bound states near the molecular scattering continuum. The tunability of the interactions between molecules opens up novel applications such as controlled chemical reactions and synthesis of ultracold complex molecules.     

Low-Dimensional Forest-Like and Desert-Like Fractal Patterns Formed in a DDAN Molecular System

Two kinds of forest-like and desert-like patterns are formed by thermal evaporation of 4-dicyanovinyl-N, Ndimethylamino-1-naphthalene （DDAN） onto SiO2 substrates. Based on thermal kinetics of the molecules on the substrate the transformation between the forest and desert patterns is due to two factors. The first one is the diffusion length, which is related to the deposition rate, the diffusion potential energy barrier and the substrate temperature. The second one is the strong interaction between the two polarity chemical groups of the molecules, which is beneficial to the formation of branches. Totally different patterns are also found on mica substrates, and are attributed to the anisotropic diffusion and the stronger interaction between DDAN molecules and the mica surface.     

Thermal desorption of interacting molecules from mixed adlayers

A Monte Carlo simulation method is used to study thermal desorption of gas molecules from mixed adlayers containing two species. The effects of lateral interactions among adatoms and initial surface coverage on the desorption spectra are examined. It is shown that attractive lateral interactions lead to sharper peaks and that desorption occurs at high temperatures, whereas repulsive interactions lead to multiple peak spectra. It is found that interactions between unlike molecules affect the spectra for species with lower desorption energy only, and that the two species desorb together only in certain cases. Lateral interactions also affect the desorption kinetics significantly and very different behavior for the two species may be obtained.     

Reproduction of a protocell by replication of a minority molecule in a catalytic reaction network

For understanding the origin of life, it is essential to explain the development of a compartmentalized structure, which undergoes growth and division, from a set of chemical reactions. In this study, a hypercycle with two chemicals that mutually catalyze each other is considered in order to show that the reproduction of a protocell with a growth-division process naturally occurs when the replication speed of one chemical is considerably slower than that of the other chemical, and molecules are crowded as a result of replication. It is observed that the protocell divides after a minority molecule is replicated at a slow synthesis rate, and thus, a synchrony between the reproduction of a cell and molecule replication is achieved. The robustness of such protocells against the invasion of parasitic molecules is also demonstrated.     

Analytical Techniques Used to Detect DNA Binding Modes of Ruthenium(II) Complexes with Extended Phenanthroline Ring

This review describes the analytical techniques used to detect DNA-probes such as Ru(II) complexes with hetero cyclic imidazo phenanthroline (IP) ligands. Studies on drug-DNA interactions are useful biochemical techniques for visualization of DNA both in vitro and in vivo. The interactions of small molecules that binds to DNA are mainly classified into two major classes, one involving covalent binding and another non-covalent binding. Covalent binding in DNA can be irreversible and may leads to inhibition of all DNA processes which subsequently leads to cell death. Usually, covalent interactions leads to permanent changes in the structure of nucleic acids. The non-covalent interaction of molecules with DNA can be due to electrostatic interaction, intercalation and groove binding. These interactions of DNA probes can be explored by various spectroscopic techniques viz. UV–visible, emission, emission quenching spectroscopy, viscosity and thermal denaturation measurements.     

Langmuir-Blodgett film and nematic interface

The orientation induced by a Langmuir-Blodgett film on a Nematic Liquid Crystal (NLC) is theoretically analyzed. We show that the effective surface energy is due to different contributions connected with steric and van der Waals interactions between the nematic and the solid substrate. The analysis shows that the Langmuir-Blodgett film orientation depends on the surface density of the molecules. The initial homeotropic orientation may become unstable giving rise to a tilted film. The average orientation of the nematic molecules is also analyzed. We show that, in the event in which the steric interaction Nematic-Langmuir-Blodgett film is very large with respect to the dispersion interaction Nematic-Substrate, the nematic orientation coincides with the one of the film. On the contrary, when the two interactions are comparable, the orientation of the two media may differ. In particular, we analyze how the stable orientation depends on the surface molecular density of the film.     

Adsorption of some substituted ethylene molecules on Pt(111) at 95 K Part 1: NEXAFS, XPS and UPS studies

The present work examines the interactions of propanoic acid, acrylic acid, acrolein and methylmethacrylate (MMA) with Pt(111) at 95 K to identify the nature of the interactions on this surface. The investigations are carried out by XPS, UPS and NEXAFS on monolayer and multilayer. Theoretical molecular orbital calculations are firstly performed to determine the nature of the bonding and antibonding orbitals of these molecules. The NEXAFS results show that the condensed multilayers of acrylic acid and acrolein are almost oriented parallel to the surface when propanoic acid and MMA are randomly oriented. The monolayer formed at 95 K for all these molecules are also oriented flat on Pt(111). However two different interaction processes are observed depending on the chemical structure of the compound: acrolein and propanoic acid are physisorbed when MMA and acrylic acid are in strong interaction with the metal but with an uncertainty on the chemisorption mode between a π-bonded state or a “di-σ like” state.     

A diffusion Monte Carlo study of small para-hydrogen clusters

An improved Monte Carlo diffusion model is used to calculate the ground state energies and chemical potentials of parahydrogen clusters of three to forty molecules, using two different p-H₂-p-H₂ interactions. The improvement is due to three-body correlations in the importance sampling, to the time step adjustment and to a better estimation of statistical errors. In contrast to path-integral Monte Carlo results, this method predicts no magic clusters other than that with thirteen molecules.      

费米原子对的玻色-爱因斯坦凝聚

通过磁场可以用原子散射的Feshbach共振来调节原子间的相互作用，使之成为排斥或吸引，以及改变作用的强度，运用这个方法可以使费米原子形成分子，也可以在多体作用下形成费米原子配对，在温度够低的条件下可以得到分子的BEC以及原子配对的凝聚体，这些现象在实验室中的实现是2004年物理学的重要成就之一，本文对此给予简短的评述。     

Electric induction interactions between molecules through fifth-order perturbation theory

Electric induction interactions in a system of N molecules of arbitrary asymmetry are examined in the first five orders of non-degenerate perturbation theory. The results are used to evaluate fourth-order induction interactions between two hydrogen fluoride molecules     

Relation between adsorption and catalysis in the case of NiO and Co3O4

Reversed flow-inverse gas chromatography is a quick, precise and effective methodology to characterize physicochemical properties of adsorbents. This is extended to the experimental measurement of the adsorption energy distribution function as well as of the differential energy of adsorption due to lateral interactions of molecules adsorbed on two catalysts, namely Co₃O₄ and NiO. Thus, the nature and the strength of the adsorbate-adsorbent and adsorbate-adsorbate interactions are extracted in order to give detailed answers to the questions: (a) where are the molecules on the heterogeneous surface and (b) which is the nature of the surface chemical bonds? Thus, adsorption of 1-butene was found to take place immediately and irreversibly. It holds a deep relation between adsorption and catalysis of 1-butene over these catalysts. As a consequence, the adsorption of 1-butene in the presence of hydrogen leads to isobutane and/or n-butane, depending on the temperature. It can be seen from the adsorption/desorption kinetic constants that the adsorption of 1-butene on Co₃O₄ is one order higher than over NiO. This fact in connection with the bigger activation energy and the lower kinetic coefficients concerning hydrogenation reaction over NiO shows that Co₃O₄ is a better catalyst for this kind of catalysis.     

活细胞中的化学物理-光学观测和控制细胞内信号转导

Cells are crowded microenvironments filled with macromolecules undergoing constant physical and chemical interactions. The physicochemical makeup of the cells affects various cellular responses, determines cell-cell interactions and influences cell decisions. Chemical and physical properties differ between cells and within cells. Moreover, these properties are subject to dynamic changes in response to environmental signals, which often demand adjustments in the chemical or physical states of intracellular molecules. Indeed, cellular responses such as gene expression rely on the faithful relay of information from the outside to the inside of the cell, a process termed signal transduction. The signal often traverses a complex path across subcellular spaces with variable physical chemistry, sometimes even influencing it. Understanding the molecular states of such signaling molecules and their intracellular environments is vital to our understanding of the cell. Exploring such intricate spaces is possible today largely because of experimental and theoretical tools. Here, we focus on one tool that is commonly used in chemical physics studies-light. We summarize recent work which uses light to both visualize the cellular environment and also control intracellular processes along the axis of signal transduction. We highlight recent accomplishments in optical microscopy and optogenetics, an emerging experimental strategy which utilizes light to control the molecular processes in live cells. We believe that optogenetics lends unprecedented spatiotemporal precision to the manipulation of physicochemical properties in biological contexts. We hope to use this work to demonstrate new opportunities for chemical physicists who are interested in pursuing biological and biomedical questions.