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Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…

Allosteric interactions occur when binding at one part of a complex affects the interactions at another part. Allostery offers a high degree of control in multi-species processes, and these interactions play a crucial role in many…

Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically modelled using either deterministic…

Ligand receptor interactions are commonly assessed through equilibrium occupancy and pharmacodynamic measures that describe binding and saturation by means of bounded response curves. Thermodynamic approaches relate binding affinity to…

The accurate screening of candidate drug ligands against target proteins through computational approaches is of prime interest to drug development efforts. Such virtual screening depends in part on methods to predict the binding affinity…

The cytoskeleton, consisting of biopolymer filaments, molecular motors, and passive crosslinking proteins, provides the internal structure of cells that facilitate movement, growth, and cell division. Understanding the microscopic…

Gradient sensing underlies important biological processes including morphogenesis, polarization, and cell migration. The precision of gradient sensing increases with the length of a detector (a cell or group of cells) in the gradient…

Adaptive gradient methods like Adagrad and its variants are widespread in large-scale optimization. However, their use of diagonal preconditioning matrices limits the ability to capture parameter correlations. Full-matrix adaptive methods,…

Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here we show that…

Predicting transcriptional responses to novel drugs provides a unique opportunity to accelerate biomedical research and advance drug discovery efforts. However, the inherent complexity and high dimensionality of cellular responses, combined…

Allosteric signaling in biological molecules, which may be viewed as specific action at a distance due to localized perturbation upon binding of ligands or changes in environmental cues, is pervasive in biology. Phenomenological MWC and KNF…

Cellular nuclei recognition serves as a fundamental and essential step in the workflow of digital pathology. However, with disparate source organs and staining procedures among histology image clusters, the scanned tiles inherently conform…

Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can…

Our ability to calculate rates of biochemical processes using molecular dynamics simulations is severely limited by the fact that the time scales for reactions, or changes in conformational state, scale exponentially with the relevant…

Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based…

Self-generated gradients (SGG) provide robust steering cues that guide cells in their long-distance expeditions during embryonic development, immune response, and cancer metastasis. Cells generate their own local, dynamic gradients by…

We propose and experimentally validate the use of rotational echo responses for obtaining the degree of molecular alignment induced in a gas. The method is independent of various parameters that are hardly accessible in most experimental…

We study the ultrasensitivity of multisite binding processes where ligand molecules can bind to several binding sites, considering more particularly recent models involving complex chemical reactions in phosphorylation systems such as…

Biomolecular thermodynamics and spectroscopy depend on relative conformer energies, local curvatures, and collective dipole fluctuations on the potential-energy surface. Conventional molecular mechanics force fields enable large-scale…

Receptor-ligand binding is a critical first step in signal transduction and the duration of the interaction can impact signal generation. In mammalian cells, clustering of receptors may be facilitated by heterogeneous zones of lipids, known…