Related papers: An Introduction to Biomolecular Simulations and Do…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
Dynamical systems see widespread use in natural sciences like physics, biology, chemistry, as well as engineering disciplines such as circuit analysis, computational fluid dynamics, and control. For simple systems, the differential…
In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…
Biomolecular force fields have been traditionally derived based on a mixture of reference quantum chemistry data and experimental information obtained on small fragments. However, the possibility to run extensive molecular dynamics…
Accurate physical modeling with 3D-printing techniques could lead to new approaches to study structure and dynamics of biological systems complementing computational methods. Computational biology has become an important part of research…
In spite of the great success that all-atom molecular dynamics simulations have seen in revealing the nature of the lipid bilayer, the interplay between a membrane's curvature and dynamics remains elusive. This is largely due to the…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
The physiological tradition of biological research analyzes biological systems using reduced descriptions much as an engineer uses a 'black box' description of an amplifier. Simple models have been used by physiologists for a very long…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
Diffusion probabilistic models have made their way into a number of high-profile applications since their inception. In particular, there has been a wave of research into using diffusion models in the prediction and design of biomolecular…
Time-resolved investigations of ultrafast electronic and molecular dynamics were not possible until recently. The typical time scale of these processes is in the picosecond to attosecond realm. The tremendous technological progress in…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
Modeling and simulation are recognized as important aspects of the scientific method for more than 70 years but its adoption in biology has been slow. Debates on its representativeness, usefulness, and whether the effort spent on such…
The simulated self-assembly of molecular building blocks into functional complexes is a key area of study in computational biology and materials science. Self-assembly simulations of proteins using physically-motivated potentials for…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
Biofilms are complex structures which are inhabited by numerous amount of different species of microorganisms. Due to their ubiquity, they influence human life on an everyday basis. It is therefore important to understand the interactions…
In this paper we present the results of a large-scale numerical investigation of structural properties of a model of cell membrane, simulated as a bilayer of flexible molecules in vacuum. The study was performed by carrying out extensive…
Unlike computation or the numerical analysis of differential equations, simulation does not have a well established conceptual and mathematical foundation. Simulation is an arguable unique union of modeling and computation. However,…