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Metaproteomics are becoming widely used in microbiome research for gaining insights into the functional state of the microbial community. Current metaproteomics studies are generally based on high-throughput tandem mass spectrometry (MS/MS)…
Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales…
We study a physical model for the interaction between general inclusions bound to fluid membranes that possess finite tension, as well as the usual bending rigidity. We are motivated by an interest in proteins bound to cell membranes that…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
Many cell functions are accomplished thanks to intracellular transport mechanisms of macromolecules along filaments. Molecular motors such as dynein or kinesin are proteins playing a primary role in these processes. The behavior of such…
The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by…
The aim of this paper is to develop suitable models for the phenomenon of cell blebbing, which allow for computational predictions of mechanical effects including the crucial interaction of the cell membrane and the actin cortex. For this…
Single-molecule pulling experiments on unstructured proteins linked to neurodegenerative diseases have measured rupture forces comparable to those for stable folded proteins. To investigate the structural mechanisms of this unexpected force…
The influenza/H1N1 virus has caused hazard in the public health of many countries. Hence, existing influenza drugs could not cope with H1N1 infection due to the high mutation rate of the virus. In this respect, new method to block the virus…
Tungsten microneedles are currently used to insert neural electrodes into living peripheral nerves. However, the biomechanics underlying these procedures is not yet well characterized. For this reason, the aim of this work was to model the…
The aim of this paper is to study two models for a bacterial population subject to antibiotic treatments. It is known that some bacteria are sensitive to antibiotics. These bacteria are in a state called persistence and each bacterium can…
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
The self-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation. The advantage of the atomistic approach is that the detailed level of description allows complete freedom in…
We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the…
The hydrodynamic interactions of a suspension of self-propelled particles are studied using a direct numerical simulation method which simultaneously solves for the host fluid and the swimming particles. A modified version of the "Smoothed…
Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. Yet it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils, or just a dangerous by-product.…
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…
We examine how the shape of cells and the geometry of experiment affect the reaction-diffusion kinetics at the binding between target and probe molecules on molecular biochips. In particular, we compare the binding kinetics for the probes…
The diffusion of molecules (penetrants) of variable size, shape, and chemistry through dense crosslinked polymer networks is a fundamental scientific problem that is broadly relevant in materials, polymer, physical and biological chemistry.…