Related papers: From proteins to grains: a journey through simple …
Biomaterial systems have allowed for the in vitro production of complex, emergent tissue behaviors that were not possible with conventional 2D culture systems allowing for analysis of the normal development as well as disease processes. We…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
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…
We study the mechanical unfolding of a simple model protein. The Langevin dynamics results are analyzed using Markov-model methods which allow to describe completely the configurational space of the system. Using transition path theory we…
The infrastructure upon which the functioning of society depends is composed of complex ecosystems of systems. Consequently, we must reason about the properties of such ecosystems, which requires that we construct models of them. There are…
All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources,…
Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable…
We propose a new material viscoelastic model and mathematical solution to simulate relaxation modulus and viscoelastic response. The model formula of relaxation modulus is extended from sigmoidal function considering nonlinear strain…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
Granular materials are involved in most industrial and environmental processes, as well as many civil engineering applications. Although significant advances have been made in understanding the statics and dynamics of cohesionless grains…
In systems biology effective models are widely used due to the complexity of biological system. They result from a coarse-graining process which employs specific assumptions. Frequently one does not start with a model taking all details…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…
This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…
Models which allow an explicit application to structurally modulated substances are reviewed within the frame of a symmetry-based approach starting from discrete lattice theory. Focus is set on models formulated in terms of local variables…
Scientists often use observational time series data to study complex natural processes, but regression analyses often assume simplistic dynamics. Recent advances in deep learning have yielded startling improvements to the performance of…
Although coarse-grained models have been widely used to explain exotic phenomena in complex fluids, such as droplet formation in living cells, these conventional approaches often fail to capture the intricate microscopic degrees of freedom…
Signal processing traditionally relies on classical statistical modeling techniques. Such model-based methods utilize mathematical formulations that represent the underlying physics, prior information and additional domain knowledge. Simple…
Granular intrusion is commonly observed in natural and human-made settings. Unlike typical solids and fluids, granular media can simultaneously display fluid-like and solid-like characteristics in a variety of intrusion scenarios. This…
While existing mathematical descriptions can accurately account for phenomena at microscopic scales (e.g. molecular dynamics), these are often high-dimensional, stochastic and their applicability over macroscopic time scales of physical…