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Mechanics and biochemical signaling are both often deregulated in cancer, leading to cancer cell phenotypes that exhibit increased invasiveness, proliferation, and survival. The dynamics and interactions of cytoskeletal components control…
Chemical reaction networks in living cells maintain precise control over thousands of metabolites despite operating far from equilibrium under constant perturbations. While mass action kinetics accurately describe the underlying dynamics,…
Fluctuations in the abundance of molecules in the living cell may affect its growth and well being. For regulatory molecules (e.g., signaling proteins or transcription factors), fluctuations in their expression can affect the levels of…
We present the multicomponent functionalized free energies that characterize the low-energy packings of amphiphilic molecules within a membrane through a correspondence to connecting orbits within a reduced dynamical system. To each…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Biomedical signals carry signature rhythms of complex physiological processes that control our daily bodily activity. The properties of these rhythms indicate the nature of interaction dynamics among physiological processes that maintain a…
For efficient application of protons and light ions in radiotherapy, detailed knowledge and realistic models of the corresponding radiobiological mechanism are necessary. Basic characteristics of this mechanism have been represented within…
The thermodynamic (TD) properties of biological membranes play a central role for living systems. It has been suggested, for instance, that nonlinear pulses such as action potentials (APs) can only exist if the membrane state is in vicinity…
We investigate dynamics of a kinetic model of inhibitory autoregulation as exemplified when a protein inhibits its own production by interfering with its messenger RNA, known in molecular biology as translational autoregulation. We first…
The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins,…
Proteases regulate various aspects of the life cycle in all organisms by cleaving specific peptide bonds. Their action is so central for biochemical processes that at least 2% of any known genome encodes for proteolytic enzymes. Here we…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
Mixtures of particles that interact through phoretic effects are known to aggregate if they belong to species that exhibit attractive self-interactions. We study self-organization in a model metabolic cycle composed of three species of…
We present a new method that enables the identification and analysis of both transition and metastable conformational states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented and studied by…
Switching of the direction of flagella rotations is the key control mechanism governing the chemotactic activity of E. coli and many other bacteria. Power-law distributions of switching times are most peculiar because their emergence cannot…
We present a three-stage probabilistic model for the progression of Chronic Myeloid Leukemia (CML), as manifested by the leukemic stem cells, progenitor cells and mature leukemic cells. This progression is captured through the process of…
The methodology named LIFE (Linear-in-Flux-Expressions) was developed with the purpose of simulating and analyzing large metabolic systems. With LIFE, the number of model parameters is reduced by accounting for correlations among the…
In a many-body localized (MBL) quantum system, the ergodic hypothesis breaks down completely, giving rise to a fundamentally new many-body phase. Whether and under which conditions MBL can occur in higher dimensions remains an outstanding…
Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different…
DNA supercoils are generated in genome regulation processes such as transcription and replication, and provide mechanical feedback to such processes. Under tension, DNA supercoil can present a coexistence state of plectonemic (P) and…