Related papers: Using Metadynamics to Reveal Extractant Conformati…
The potential of mean-field decomposition techniques in interpreting electronic transitions in molecules is explored, particularly, the usefulness of these for offering computational signatures of different classes of such excitations. When…
The present paper proposes an adaptive biasing potential for the computation of free energy landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells…
Describing chemical reactions in solution on a molecular level is a challenging task due to the high mobility of weakly interacting solvent molecules which requires configurational sampling. For instance, polar and protic solvents can…
We present a novel route to constructing cost-efficient semi-empirical approximations for the non-additive kinetic energy in subsystem density functional theory. The developed methodology is based on the use of Slater determinants composed…
Metadynamics, a member of the `flat histogram' class of advanced sampling algorithms, has been widely used in molecular simulations to drive the exploration of states separated by high free energy barriers and promote comprehensive sampling…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
In this paper, we propose an energy decomposition method combined with an HLL Riemann solver that includes an additional dissipation term in the energy equation to improve the numerical stability of the fully implicit, time-evolving coronal…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
Context: Relaxation theory offers a straightforward method for estimating the energy that is released when a magnetic field becomes unstable, as a result of continual convective driving. Aims: We present new results obtained from nonlinear…
In this work, we study the dynamics of complex systems with time-dependent transition rates, focusing on $p$-adic analysis in modeling such systems. Starting from the master equation that governs the stochastic dynamics of a system with a…
Dynamic density functional theory (DDFT) is a promising approach for predicting the structural evolution of a drying suspension containing one or more types of colloidal particles. The assumed free-energy functional is a key component of…
We formally extend the energy landscape approach for the thermodynamics of liquids to account for saddle points. By considering the extensive nature of macroscopic potential energies, we derive the scaling behavior of saddles with system…
The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While…
Free energy landscapes provide insights into conformational ensembles of biomolecules. In order to analyze these landscapes and elucidate mechanisms underlying conformational changes, there is a need to extract metastable states with…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
Molecular Density Functional Theory (MDFT) offers an efficient implicit- solvent method to estimate molecule solvation free-energies whereas conserving a fully molecular representation of the solvent. Even within a second order ap-…
Reactive chemistry of molecular hydrogen at surfaces, notably dissociative sticking and hydrogen evolution, plays a crucial role in energy storage and fuel cells. Theoretical studies can help to decipher underlying mechanisms and reaction…
Segmentation, a new approach based on successive edge contraction is introduced for extract method refactoring. It targets identification of distinct functionalities implemented within a method. Segmentation builds upon data and control…
Power dissipation and energy consumption have become one of the most important problems in the design of processors today. This is especially true in power-constrained environments, such as embedded and mobile computing. While lowering the…
We show that the analytic structure of the dynamical xc kernels of semiconductors and insulators can be sensed in terms of its poles which mark physically relevant frequencies of the system where the counter-phase motion of discrete…