Related papers: Optimizations of protein force fields
Understanding the microstuctural evolution during the sintering process is of high relevance as it is a key part in many industrial manufacturing processes. Simulations are one avenue to achieve this understanding, especially field-resolved…
In this work we introduce new scalar field models and study the defect solutions they may engender. The investigation is based on the deformation procedure, which greatly simplify the calculations, leading us to new models together with the…
Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transition states for chemical reactions using quantum chemical…
To address the computational challenges of ab initio molecular dynamics and the accuracy limitations of empirical force fields, the introduction of machine learning force fields has proven effective in various systems including metals and…
We empirically evaluate the finite-time performance of several simulation-optimization algorithms on a testbed of problems with the goal of motivating further development of algorithms with strong finite-time performance. We investigate if…
In the last ten years, the phase-field method has gained much attention as a novel method to simulate fracture due to its straightforward way allowing to cover crack initiation and propagation without additional conditions. More recently,…
An approach to the mechanical behaviour of textile composites at the scale of their constituting fibres, using an implicit finite element simulation code, is proposed in this chapter. The approach is based on efficient methods and…
Large parallel gains in the development of both computational resources as well as sampling methods have now made it possible to simulate dissociation events in ligand-protein complexes with all--atom resolution. Such encouraging progress,…
We present a detailed study of the performance and reliability of design procedures based on energy minimization. The analysis is carried out for model proteins where exact results can be obtained through exhaustive enumeration. The…
Building on substantial foundational progress in understanding the effect of a small body's self-field on its own motion, the past 15 years has seen the emergence of several strategies for explicitly computing self-field corrections to the…
This paper presents the latest trends in the powering of particle accelerators. A series of solutions is proposed for responding to the challenges of high performance machines. This paper covers the domains of magnetic field uncertainty,…
Gaussian process (GP) emulator has been used as a surrogate model for predicting force field and molecular potential, to overcome the computational bottleneck of molecular dynamics simulation. Integrating both atomic force and energy in…
Simulation Optimization (SO) refers to the optimization of an objective function subject to constraints, both of which can be evaluated through a stochastic simulation. To address specific features of a particular simulation---discrete or…
We apply the general protocol of parameter optimization (Lee, J. et al. Phys. Chem. B 2001, 105, 7291) to the UNRES potential. In contrast to the earlier works where only the relative weights of various interaction terms were optimized, we…
Hybrid particle-field methods are computationally efficient approaches for modelling soft matter systems. So far applications of these methodologies have been limited to constant volume conditions. Here, we reformulate particle-field…
This chapter reviews how molecular dynamics simulations, experimental data, and Markov state models can synergize to map-out the mechanism of protein-protein association and dissociation.
Many proteins carry out their biological functions by forming the characteristic tertiary structures. Therefore, the search of the stable states of proteins by molecular simulations is important to understand their functions and…
The application of optimization techniques derived from the study of Euclidean full Steiner Trees to macromolecules like proteins is reported in the present work. We shall use the concept of Euclidean Steiner Ratio Function (SRF) as a good…
This article deals with the prediction of thermomechanical properties of fiber reinforced composites using several micromechanics models. These include strength of material approach, Halpin-Tsai equations, multi-phase mechanics of materials…
In recent years, several swarm intelligence optimization algorithms have been proposed to be applied for solving a variety of optimization problems. However, the values of several hyperparameters should be determined. For instance, although…