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The generation of small molecule candidate (ligand) binding poses in its target protein pocket is important for computer-aided drug discovery. Typical rigid-body docking methods ignore the pocket flexibility of protein, while the more…
In his seminal paper on morphogenesis (1952), Alan Turing demonstrated that different spatio-temporal patterns can arise due to instability of the homogeneous state in reaction-diffusion systems, but at least two species are necessary to…
Chronic diseases can greatly benefit from bioelectronic medicine approaches. Neuromorphic electronic circuits present ideal characteristics for the development of brain-inspired low-power implantable processing systems that can be…
We study the Swift-Hohenberg equation - a paradigm model for pattern formation - with "large" spatially periodic coefficients and find a Turing bifurcation that generates patterns whose leading order form is a Bloch wave modulated by…
A ternary reaction-diffusion model for early HIV infection dynamics, incorporating logistic growth of target cells, is introduced. According to in vitro and in vivo studies, random movement of target cells, infected cells, and virions and a…
A model of pattern formation in living systems is presented. The pattern is achieved by the sequential interaction of two signaling pathways. The coupling of the pattern to the (thick) epithelial sheet changes is given, when the Gauss…
Organogenesis has been studied for decades, but fundamental questions regarding the control of growth and shape remain unsolved. We have recently shown that of all proposed mathematical models only ligand-receptor based Turing models…
We rigorously prove the bifurcation of slow-moving pattern interfaces with general direction in a two-dimensional Swift-Hohenberg-type model close to a Turing instability for a large class of nonlinearities. These interfaces describe the…
A study of principle is conducted on the inclusion of the fermionic determinant as a Metropolis acceptance correction. It is carried out in the 2-D Schwinger model to prepare later applications to the Schr"odinger functional. A mixed…
Turing's mechanism is often invoked to explain periodic patterns in nature, although direct experimental support is scarce. Turing patterns form in reaction-diffusion systems when the activating species diffuse much slower than the…
Drifting pattern domains (DPDs), moving localized patches of traveling waves embedded in a stationary (Turing) pattern background and vice versa, are observed in simulations of a reaction-diffusion model with nonlocal coupling. Within this…
The mechanics of complex soft matter often cannot be understood in the classical physical frame of flexible polymers or rigid rods. The underlying constituents are semiflexible polymers, whose finite bending stiffness ($\kappa$) leads to…
Piebaldism usually manifests as white areas of fur, hair or skin due to the absence of pigment-producing cells in those regions. The distribution of the white and colored zones does not follow the classical Turing patterns. Here we present…
Various theoretical studies have been carried out to infer relevant protein-protein interactions among pathogens and their hosts. Such studies are generally based on preferential attachment of bacteria / virus to their human receptor…
We present a novel machine learning approach to understanding conformation dynamics of biomolecules. The approach combines kernel-based techniques that are popular in the machine learning community with transfer operator theory for…
Emergent pattern formation in self-propelled particle (SPP) systems is extensively studied because it addresses a range of swarming phenomena which occur without leadership. Here we present a dynamic SPP model in which a sensory blind zone…
Shapes of biological membranes are dynamically regulated in living cells. Although membrane shape deformation by proteins at thermal equilibrium has been extensively studied, nonequilibrium dynamics have been much less explored. Recently,…
Within the germinal center in follicles, B-cells proliferate, mutate and differentiate, while being submitted to a powerful selection~: a micro-evolutionary mechanism at the heart of adaptive immunity. A new foreign pathogen is confronted…
Capturing intricate biological phenomena often requires multiscale modeling where coarse and inexpensive models are developed using limited components of expensive and high-fidelity models. Here, we consider such a multiscale framework in…
Macrocyclic peptides are an emerging therapeutic modality, yet computational approaches for accurately sampling their diverse 3D ensembles remain challenging due to their conformational diversity and geometric constraints. Here, we…