相关论文: A Computational Methodology to Screen Activities o…

The time evolution of the thermally activated decay rates is considered. This evolution is of particular importance for the recent nanoscale experiments discussed in the literature, where the potential barrier is relatively low (or the…

When examining dynamics occurring at non-zero temperatures, both energy and entropy must be taken into account while describing activated barrier crossing events. Furthermore, good reaction coordinates need to be constructed to describe…

The yardstick of new first-principles approaches to key points on reaction paths at metal surfaces is chemical accuracy compared to reliable experiment. By this we mean that such values as the activation barrier are required to within 1…

Activity cliff prediction - identifying positions where small structural changes cause large potency shifts - has been a persistent challenge in computational medicinal chemistry. This work focuses on a parsimonious definition: which small…

A variational approach is used to calculate free energy and conformational properties in polyelectrolytes. The true bond and Coulomb potentials are approximated by a trial isotropic harmonic energy containing monomer-monomer force constants…

Molecular dynamics (MD) simulations have transformed our understanding of the nanoscale, driving breakthroughs in materials science, computational chemistry, and several other fields, including biophysics and drug design. Even on exascale…

Crystallization from a supercooled liquid initially proceeds via the formation of a small solid embryo (nucleus), which requires surmounting an activation barrier. This phenomenon is most easily studied by numerical simulation, using…

Computational catalysis is playing an increasingly significant role in the design of catalysts across a wide range of applications. A common task for many computational methods is the need to accurately compute the adsorption energy for an…

Quantum-chemical simulations are essential for predicting energies of chemical reactions. Accurately solving the many-body Schr\"odinger equation for reagent and product states of most relevant chemical process is, however, unfeasible.…

Adiabatic quantum optimization offers a new method for solving hard optimization problems. In this paper we calculate median adiabatic times (in seconds) determined by the minimum gap during the adiabatic quantum optimization for an NP-hard…

The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of…

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,…

We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…

Fixed node diffusion Monte Carlo (DMC) has been performed on a test set of forward and reverse barrier heights for 19 non-hydrogen-transfer reactions, and the nodal error has been assessed. The DMC results are robust to changes in the nodal…

The proliferative activity of breast tumors, which is routinely estimated by counting of mitotic figures in hematoxylin and eosin stained histology sections, is considered to be one of the most important prognostic markers. However, mitosis…

We present an Adaptively Biased Molecular Dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using non-equilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling…

Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…

Machine-learned potential energy surfaces (PESs) for molecules with more than 10 atoms are typically forced to use lower-level electronic structure methods such as density functional theory and second-order Moller-Plesset perturbation…

The rare event acceleration method BXDE is interfaced in the present work with the automated reaction discovery method AutoMeKin. To test the efficiency of the combined AutoMeKin-BXDE procedure, the ozonolysis of a-pinene is studied in…

In this work, we introduce a simple modification of the Monte Carlo algorithm, which we call step Monte Carlo (sMC). The sMC approach allows to simulate processes far from equilibrium and obtain information about the dynamic properties of…