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Although ligand-binding sites in many proteins contain a high number density of charged side chains that can polarize small organic molecules and influence binding, the magnitude of this effect has not been studied in many systems. Here, we…
Many of the cell membrane vital functions are achieved by the self-organization of the proteins and biopolymers embedded in it. The protein dynamics are in part determined by its drag. A large number of these proteins can polymerize to form…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
Eukaryotic cells and intracellular pathogens such as bacteria or viruses utilize the actin polymerization machinery to propel themselves forward. Thereby, the onset of motion and choice of direction may be the result of a spontaneous…
Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species…
We derive the constitutive equations of an active polar gel from a model for the dynamics of elastic molecules that link polar elements. Molecular binding kinetics induces the fluidization of the material, giving rise to Maxwell…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…
The forces that mixtures of motorized and passive crosslinking proteins collectively generate between cytoskeletal filaments within our cells are the key drivers of active cellular mechanics. Despite their importance, a unified theory to…
Systems with two species of active molecular motors moving on (cytoskeletal) filaments into opposite directions are studied theoretically using driven lattice gas models. The motors can unbind from and rebind to the filaments. Two motors…
Synchronous and directed ciliary beating in trachea allows transport and ejection of virus and dust from the body. This ciliary function depends on the coordinated configuration of basal bodies (root of cilia) in apical cell membrane.…
Collective cell migration contributes to embryogenesis, wound healing and tumor metastasis. Cell monolayer migration experiments help understanding what determines the movement of cells far from the leading edge. Inhibiting cell…
The mechanisms driving the collective movement of cells remain poorly understood. To contribute toward resolving this mystery, a model was formulated to theoretically explore the possible functions of polarized cell-cell adhesion in…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
Membrane deformation inside living cells is crucial for the proper shaping of various intracellular organelles and is necessary during the fission/fusion processes that allow membrane recycling and transport (e.g. endocytosis). Proteins…
We have used numerical simulations to investigate how the properties of motor proteins control the dynamical behavior of a driven flexible filament. The filament is pinned at one end and positioned on top of a patch of anchored motor…
Recent biological experiments have shown that certain types of cells are able to move in structured and confined environment even without the activation of focal adhesion. Focusing on this particular phenomenon and based on previous works,…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
The more we learn about the cytoplasm of cells, the more we realise that the cytoplasm is not uniform but instead is highly inhomogeneous. In any inhomogeneous solution, there are concentration gradients, and particles move either up or…
Spatial organization of proteins in cells is important for many biological functions. In general, the nonlinear, spatially coupled models for protein-pattern formation are only accessible to numerical simulations, which has limited insight…