Printed From BioPortfolio.com

02:08 EDT 24th October 2017 | BioPortfolio

The US National Library of Medicine and National Institutes of Health manage PubMed.gov which comprises of more than 21 million records, papers, reports for biomedical literature, including MEDLINE, life science and medical journals, articles, reviews, reports and books. BioPortfolio aims to publish relevant information on published papers, clinical trials and news associated with users selected topics.

For example view all recent relevant publications on Epigenetics and associated publications and clincial trials.

Origin of diverse time scales in the protein hydration layer solvation dynamics: A simulation study.

In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics, we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems, namely, lysozyme, myoglobin, and sweet protein monellin. In these experiments, we mutate the charges of the neighbouring amino acid side chains of certain natural probes (tryptophan) and also freeze the side chain motions. In order to distinguish between different contributions, we dec...

Recent single-molecule experiments probed transition paths of biomolecular folding and, in particular, measured the time biomolecules spend while crossing their free energy barriers. A surprising finding from these studies is that the transition barriers crossed by transition paths, as inferred from experimentally observed transition path times, are often lower than the independently determined free energy barriers. Here we explore memory effects leading to anomalous diffusion as a possible origin of this d...

The diffusion of a Ga atom on GaAs(001)β2(2 × 4): Local superbasin kinetic Monte Carlo.

We use first-principles density-functional theory to characterize the binding sites and diffusion mechanisms for a Ga adatom on the GaAs(001)β2(2 × 4) surface. Diffusion in this system is a complex process involving eleven unique binding sites and sixteen different hops between neighboring binding sites. Among the binding sites, we can identify four different superbasins such that the motion between binding sites within a superbasin is much faster than hops exiting the superbasin. To describe diffusion, w...

Nucleation and growth of copper selective-area atomic layer deposition on palladium nanostructures.

The nucleation and growth of copper atomic layer deposition (ALD) on palladium have been investigated for applications in nanoscale devices. Palladium nanostructures were fabricated by electron beam lithography and range in size from 250 nm to 5 μm, prepared on oxidized silicon wafers. Copper ALD using Cu(thd)2(s) and H2(g) as reactants was carried out to selectively deposit copper on palladium seeded regions to the exclusion of surrounding oxide surfaces. Nuclei sizes and densities have been quantified by...

The methyl carbocation is ubiquitous in gaseous environments, such as planetary ionospheres, cometary comae, and the interstellar medium, as well as combustion systems and plasma setups for technological applications. Here we report on a joint experimental and theoretical study on the mechanism of the reaction CH3(+) + CH3CCCH3 (but-2-yne, also known as dimethylacetylene), by combining guided ion beam mass spectrometry experiments with ab initio calculations of the potential energy hypersurface. Such a reac...

The association and dissociation of particles via specific anisotropic interactions is a fundamental process, both in biology (proteins) and in soft matter (colloidal patchy particles). The presence of alternative binding sites can lead to multiple productive states and also to non-productive "decoy" or intermediate states. Besides anisotropic interactions, particles can experience non-specific isotropic interactions. We employ single replica transition interface sampling to investigate how adding a non-pro...

Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways.

The calculation of minimum energy or minimum free energy paths is an important step in the quantitative and qualitative studies of chemical and physical processes. The computations of these coordinates present a significant challenge and have attracted considerable theoretical and computational interest. Here we present a new local-global approach to study reaction coordinates, based on a gradual optimization of an action. Like other global algorithms, it provides a path between known reactants and products...

Communication: Master equations for electron transport: The limits of the Markovian limit.

Master equations are increasingly popular for the simulation of time-dependent electronic transport in nanoscale devices. Several recent Markovian approaches use "extended reservoirs"-explicit degrees of freedom associated with the electrodes-distinguishing them from many previous classes of master equations. Starting from a Lindblad equation, we develop a common foundation for these approaches. Due to the incorporation of explicit electrode states, these methods do not require a large bias or even "true Ma...

Heterogeneous catalytic reactions on surface and interfaces are renowned for ample intermediate adsorbates and complex reaction networks. The common practice to reveal the reaction mechanism is via theoretical computation, which locates all likely transition states based on the pre-guessed reaction mechanism. Here we develop a new theoretical method, namely, stochastic surface walking (SSW)-Cat method, to resolve the lowest energy reaction pathway of heterogeneous catalytic reactions, which combines our rec...

Characterization of the 18.280(-)-a(3)Δ1 (0,0) band of tantalum nitride, TaN.

The [18.28]0(-)-a(3)Δ1 (0,0) band near 647 nm of tantalum nitride, TaN, has been recorded and analyzed field-free and in the presence of static electric and magnetic fields. The fine and hyperfine parameters for the a(3)Δ1 and [18.28]0(-) states are determined. The (181)Ta(I = 7/2) axial nuclear electric quadrupole coupling constant, eQq0, and the effective magnetic hyperfine coupling constant, h1, are used to garner insight into the nature of electronic states. The Stark tuning of the P(2) and Q(1) lines...

Interrogating the Becke'05 density functional for non-locality information.

In two papers, Becke [J. Chem. Phys. 119, 2972 (2003) and J. Chem. Phys. 122, 064101 (2005)] introduced Kohn-Sham density-functional approximations for static and dynamical correlation to be partnered with 100 percent exactly computed exchange. Known as "B05," this was the first non-local correlation model designed to work with the full non-locality of exact (or Hartree-Fock) exchange. Non-locality issues, often referred to as the "delocalization" problem, are among the most vexing problems in density-funct...

An asymmetric mesoscopic model for single bulges in RNA.

Simple one-dimensional DNA or RNA mesoscopic models are of interest for their computational efficiency while retaining the key elements of the molecular interactions. However, they only deal with perfectly formed DNA or RNA double helices and consider the intra-strand interactions to be the same on both strands. This makes it difficult to describe highly asymmetric structures such as bulges and loops and, for instance, prevents the application of mesoscopic models to determine RNA secondary structures. Here...

For understanding the structure, dynamics, and thermal stability of (AgAu)55 nanoalloys, knowledge of the composition-temperature (c-T) phase diagram is essential due to the explicit dependence of properties on composition and temperature. Experimentally, generating the phase diagrams is very challenging, and therefore theoretical insight is necessary. We use an artificial neural network potential for (AgAu)55 nanoalloys. Predicted global minimum structures for pure gold and gold rich compositions are lower...

Nudged elastic band calculations accelerated with Gaussian process regression.

Minimum energy paths for transitions such as atomic and/or spin rearrangements in thermalized systems are the transition paths of largest statistical weight. Such paths are frequently calculated using the nudged elastic band method, where an initial path is iteratively shifted to the nearest minimum energy path. The computational effort can be large, especially when ab initio or electron density functional calculations are used to evaluate the energy and atomic forces. Here, we show how the number of such e...

The reaction path of a mechanically induced chemical transformation changes under stress. It is well established that the force-induced structural changes of minima and saddle points, i.e., the movement of the stationary points on the original or stress-free potential energy surface, can be described by a Newton Trajectory (NT). Given a reactive molecular system, a well-fitted pulling direction, and a sufficiently large value of the force, the minimum configuration of the reactant and the saddle point confi...

The threshold algorithm: Description of the methodology and new developments.

Understanding the dynamics of complex systems requires the investigation of their energy landscape. In particular, the flow of probability on such landscapes is a central feature in visualizing the time evolution of complex systems. To obtain such flows, and the concomitant stable states of the systems and the generalized barriers among them, the threshold algorithm has been developed. Here, we describe the methodology of this approach starting from the fundamental concepts in complex energy landscapes and ...

Non-equilibrium reactive flux: A unified framework for slow and fast reaction kinetics.

The flux formulation of reaction rate theory is recast in terms of the expectation value of the reactive flux with an initial condition that corresponds to a non-equilibrium, factorized reactant density. In the common case of slow reactive processes, the non-equilibrium expression reaches the plateau regime only slightly slower than the equilibrium flux form. When the reactants are described by a single quantum state, as in the case of electron transfer reactions, the factorized reactant density describes t...

Reaction pathways in atomistic models of thin film growth.

The atomistic processes that form the basis of thin film growth often involve complex multi-atom movements of atoms or groups of atoms on or close to the surface of a substrate. These transitions and their pathways are often difficult to predict in advance. By using an adaptive kinetic Monte Carlo (AKMC) approach, many complex mechanisms can be identified so that the growth processes can be understood and ultimately controlled. Here the AKMC technique is briefly described along with some special adaptions t...

Coarse-grained models have increasingly been used in large-scale particle-based simulations. However, due to their lack of degrees of freedom, it is a priori unlikely that they straightforwardly represent thermal properties with the same accuracy as their atomistic counterparts. We take a first step in addressing the impact of liquid coarse-graining on interfacial heat conduction by showing that an atomistic and a coarse-grained model of water may yield similar values of the Kapitza conductance on few-layer...

Preface: Special Topic on Reaction Pathways.

This Special Topic Issue on Reaction Pathways collects original research articles illustrating the state of the art in the development and application of methods to describe complex chemical systems in terms of relatively simple mechanisms and collective coordinates. A broad range of applications is presented, spanning the sub-fields of biophysics and material science, in an attempt to showcase the similarities in the formulation of the approaches and highlight the different needs of the different applicati...

A Markov state modeling analysis of sliding dynamics of a 2D model.

Non-equilibrium Markov State Modeling (MSM) has recently been proposed by Pellegrini et al. [Phys. Rev. E 94, 053001 (2016)] as a possible route to construct a physical theory of sliding friction from a long steady state atomistic simulation: the approach builds a small set of collective variables, which obey a transition-matrix-based equation of motion, faithfully describing the slow motions of the system. A crucial question is whether this approach can be extended from the original 1D small size demo to l...

Ions in high salt solutions have a strong propensity to form polydisperse ion aggregates with broad size and shape distributions. In a series of previous comparative investigations using femtosecond IR pump-probe spectroscopy, molecular dynamics simulation, and graph theoretical analysis, we have shown that there exists a morphological difference in the structures of ion aggregates formed in various salt solutions. As salt concentration increases, the ions in high salt solutions form either cluster-like str...

Predicting reaction coordinates in energy landscapes with diffusion anisotropy.

We consider a range of model potentials with metastable states undergoing molecular dynamics coupled to a thermal bath in the high friction regime and consider how the optimal reaction coordinate depends on the diffusion anisotropy. For this we use our recently proposed method "spectral gap optimization of order parameters (SGOOP)" [P. Tiwary and B. J. Berne, Proc. Natl. Acad. Sci. U. S. A. 113, 2839 (2016)]. We show how available information about dynamical observables in addition to static information can...

Non-adiabatic vibrational-electronic resonance in the excited electronic states of natural photosynthetic antennas drastically alters the adiabatic framework, in which electronic energy transfer has been conventionally studied, and suggests the possibility of exploiting non-adiabatic dynamics for directed energy transfer. Here, a generalized dimer model incorporates asymmetries between pigments, coupling to the environment, and the doubly excited state relevant for nonlinear spectroscopy. For this generaliz...