Related papers: Principles for optimal cooperativity in allosteric…
The study of protein mass transport via atomistic simulation requires time and length scales beyond the computational capabilities of modern computer systems. The raspberry model for colloidal particles in combination with the mesoscopic…
The spatiotemporal oscillation patterns of the proteins MinD and MinE are used by the bacterium E. coli to sense its own geometry. Strikingly, both computer simulations and experiments have recently shown that for the same geometry of the…
This work studies the role of inter-user device-to-device (D2D) cooperation for improving physical-layer secret communication in multi-user downlink systems. It is assumed that there are out-of-band D2D channels, on each of which a selected…
The energetic optimization problem, e.g., searching for the optimal switch- ing protocol of certain system parameters to minimize the input work, has been extensively studied by stochastic thermodynamics. In current work, we study this…
Using techniques borrowed from statistical physics and neural networks, we determine the parameters, associated with a scoring function, that are chosen optimally to ensure complete success in threading tests in a training set of proteins.…
Robustness, the ability of a system to maintain performance under significant and unanticipated environmental changes, is a critical property for robotic systems. While biological systems naturally exhibit robustness, there is no…
This thesis is concerned with the design of distributed algorithms for solving optimization problems. We consider networks where each node has exclusive access to a cost function, and design algorithms that make all nodes cooperate to find…
Proteins are the workhorse molecules of the cell and perform their biological functions by binding to other molecules through physical contact. Protein function is then regulated through coupling of bindings on the protein (allosteric…
Topology optimization (TO) has experienced a dramatic development over the last decades aided by the arising of metamaterials and additive manufacturing (AM) techniques, and it is intended to achieve the current and future challenges. In…
Adhering cells actively probe the mechanical properties of their environment and use the resulting information to position and orient themselves. We show that a large body of experimental observations can be consistently explained from one…
Many biological systems perform close to their physical limits, but promoting this optimality to a general principle seems to require implausibly fine tuning of parameters. Using examples from a wide range of systems, we show that this…
The plasticity of amorphous solids undergoing shear is characterized by quasi-localized rearrangements of particles. While many models of plasticity exist, the precise relationship between plastic dynamics and the structure of a particle's…
The complex physics and numerous failure modes of structural impact creates challenges when designing for impact resistance. While simple geometries of layered material are conventional, advances in 3D printing and additive manufacturing…
Energy efficiency is gaining importance in wireless communication networks which have nodes with limited energy supply and signal processing capabilities. We present a numerical study of cooperative communication scenarios based on simple…
Most sensory cells use surface receptors to detect environmental stimuli and initiate downstream signaling. Cooperative interactions among sensory receptors is known to play a crucial role in enhancing the sensitivity of biochemical…
This paper is motivated by the complex blister patterns sometimes seen in thin elastic films on thick, compliant substrates. These patterns are often induced by an elastic misfit which compresses the film. Blistering permits the film to…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
Simulated annealing is an effective and general means of optimization. It is in fact inspired by metallurgy, where the temperature of a material determines its behavior in thermodynamics. Likewise, in simulated annealing, the actions that…
Plastic deformation of crystalline and amorphous matter often involves intermittent local strain burst events. To understand the physical background of the phenomenon a minimal stochastic mesoscopic model was introduced, where…
Using a simulated annealing, we examine a bipartitioning of small worlds obtained by adding a fraction of randomly chosen links to a one-dimensional chain or a square lattice. Models defined on small worlds typically exhibit a mean-field…