Search results for " Molecular modeling"
showing 10 items of 76 documents
Non-reversible Monte Carlo simulations of spin models
2011
Abstract Monte Carlo simulations are used to study simple systems where the underlying Markov chain satisfies the necessary condition of global balance but does not obey the more restrictive condition of detailed balance. Here, we show that non-reversible Markov chains can be set up that generate correct stationary distributions, but reduce or eliminate the diffusive motion in phase space typical of the usual Monte Carlo dynamics. Our approach is based on splitting the dynamics into a set of replicas with each replica representing a biased movement in reaction-coordinate space. This introduction of an additional bias in a given replica is compensated for by choosing an appropriate dynamics …
On the adoption of the Monte Carlo method to solve one-dimensional steady state thermal diffusion problems for non-uniform solids
2013
Abstract The present paper is focussed on the investigation of the potential adoption of the Monte Carlo method to solve one-dimensional, steady state, thermal diffusion problems for continuous solids characterised by an isotropic, space-dependent conductivity tensor and subjected to non-uniform heat power deposition. To this purpose the steady state form of Fourier’s heat diffusion equation relevant to a continuous, heterogeneous and isotropic solid, undergoing a space-dependent heat power density has been solved in a closed analytical form for the general case of Cauchy’s boundary conditions. The thermal field obtained has been, then, put in a peculiar functional form, indicating that it …
Monte Carlo Simulation of Crystal-Liquid Phase Coexistence
2016
When a crystal nucleus is surrounded by coexisting fluid in a finite volume in thermal equilibrium, the thermodynamic properties of the fluid (density, pressure, chemical potential) are uniquely related to the surface excess free energy of the nucleus. Using a model for weakly attractive soft colloidal particles, it is shown that this surface excess free energy can be determined accurately from Monte Carlo simulations over a wide range of nucleus volumes, and the resulting nucleation barriers are completely independent from the size of the total volume of the system. A necessary ingredient of the analysis, the pressure at phase coexistence in the thermodynamic limit, is obtained from the in…
PET/PEN Blends of Industrial Interest as Barrier Materials. Part I. Many-Scale Molecular Modeling of PET/PEN Blends
2006
Mesoscale molecular simulations, based on parameters obtained through atomistic molecular dynamics and Monte Carlo calculations, have been used for modeling and predicting the behavior of PET/PEN blends. Different simulations have been performed in order to study and compare pure homopolymer blends with blends characterized by the presence of PET/PEN block copolymers acting as compatibilizer. A many-scale molecular modeling strategy was devised to evaluate PET/PEN blend characteristics, simulate phase segregation in pure PET/PEN blends, and demonstrate the improvement of miscibility due to the presence of the transesterification reaction products. The behavior of distribution densities and …
A new strategy for effective learning in population Monte Carlo sampling
2016
In this work, we focus on advancing the theory and practice of a class of Monte Carlo methods, population Monte Carlo (PMC) sampling, for dealing with inference problems with static parameters. We devise a new method for efficient adaptive learning from past samples and weights to construct improved proposal functions. It is based on assuming that, at each iteration, there is an intermediate target and that this target is gradually getting closer to the true one. Computer simulations show and confirm the improvement of the proposed strategy compared to the traditional PMC method on a simple considered scenario.
Monte Carlo tests of theoretical predictions for critical phenomena: still a problem?
2000
Two Monte Carlo studies of critical behavior in ferromagnetic Ising models are described: the first one deals with the crossover from the Ising class to the mean field class, when the interaction range increases. The second study deals with the finite size behavior at dimensionalities above the marginal dimension where Landau theory applies. The numerical results are compared to pertinent theoretical predictions, and unsolved problems are briefly described.
Synthesis of site-heterologous haptens for high-affinity anti-pyraclostrobin antibody generation.
2011
The design and synthesis of functional chemical derivatives of small organic molecules is usually a key step for the intricate production of a variety of bioconjugates. In this respect, the derivatization site at which the spacer arm is introduced in immunizing conjugates constitutes a highly critical parameter for the generation of high-affinity and selective antibodies. However, due to the usual complexity of the required synthetic procedures, the appropriate comparison of alternative tethering positions has often been neglected. In the present study, meticulous strategies were followed to prepare synthetic derivatives of pyraclostrobin with the same linkers located at diverse rationally-…
DNA minor groove binders: an overview on molecular modeling and QSAR approaches
2007
Molecular recognition of DNA by small molecules and proteins is a fundamental problem in structural biology and drug design. Understanding of recognition in both sequence-selective and sequence neutral ways at the level of successful prediction of binding modes and site selectivity will be instrumental for improvements in the design and synthesis of new molecules as potent and selective gene-regulatory drugs. Minor groove is the target of a large number of non-covalent binding agents. DNA binding with specific sequences, mostly AT, takes place by means of a combination of directed hydrogen bonding to base pair edges, van der Waals interactions with the minor groove walls and generalized ele…
H−ZSM-5 Modified Zeolite: Quantum Chemical Models of Acidic Sites
2007
A ZSM-5 fragment, containing 52 tetrahedral moieties, each of them formed by one silicon or one aluminum atom surrounded by four oxygen atoms, was employed to model (52T systems) by quantum chemical calculations (i) the influence of the positions of the acidic sites on the energetics of 22 aluminum monosubstituted and bisubstituted 52T acidic zeolite (H-ZSM-5) systems and (ii) the local adsorption properties and acidic strength of the corresponding -OH sites. The energetics and the structural properties of simpler acid H-ZSM-5 systems containing only five Tetrahedral moieties (5T systems) were also modeled for comparison. B3LYP/6-31G(d,p) partial geometry optimization routines were performe…
Statistical characterization of self-assembled charged nanoparticle structures
2013
We propose a novel approach for description of dynamics of nanostructure formation for a system consisting of oppositely charged particles. The combination of numerical solution of analytical Bogolyubov–Born–Green–Kirkwood–Yvon (BBGKY) type equation set with reverse Monte Carlo (RMC) method allows us to overcome difficulties of standard approaches, such as kinetic Monte Carlo or Molecular Dynamics, to describe effects of long-range Coulomb interactions. Moreover, this allows one to study the system dynamics on realistic time and length scales. We applied this method to a simple short-range Lenard–Jones (LJ)-like three- (3D) and two-dimensional (2D) system combining the long-range Coulomb an…