Related papers: Optimal rectification without forward-current supp…
Hybrid-excited electrical machines aim to combine the advantages of permanent magnet machines (high efficiency and torque density) with those of separately excited machines (ease of flux-weakening at high speed). These machines are of…
Molecular chaperones are machines that consume copious amount of ATP to drive misfolded proteins or RNA to fold into functionally competent native states. Because the folding landscapes of biomolecules with complex native state topology are…
We study the first-passage-time (FPT) properties of an active Brownian particle under stochastic resetting to its initial configuration, comprising its position and orientation, to reach an absorbing wall in two dimensions. Coupling a…
The ability to manipulate individual atoms and molecules using a scanning tunnelling microscope (STM) has been crucial for the development of a vast array of atomic scale devices and structures ranging from nanoscale motors and switches to…
This paper presents a two-phase protein folding optimization on a three-dimensional AB off-lattice model. The first phase is responsible for forming conformations with a good hydrophobic core or a set of compact hydrophobic amino acid…
In this paper, we present the periodic modifier-adaptation formulation of the dynamic real time optimization. The proposed formulation uses gradient information to update the problem with affine modifiers so that, upon convergence, its…
Recent quantum algorithms pertaining to electronic structure theory primarily focus on threshold-based dynamic construction of ansatz by selectively including important many-body operators. These methods can be made systematically more…
The concept of single molecule rectifiers proposed in a theoretical work by Aviram and Ratner in 1974 was the starting point of the now vibrant field of molecular electronics. In the meantime, a built-in asymmetry in the conductance of…
Using the analytical Fick-Jacobs approximation formalism and extensive Brownian dynamics simulations we study particle transport through two-dimensional periodic channels with triangularly shaped walls. Directed motion is caused by the…
Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here we combine complementary computational/theoretical…
This paper proposes Bayes-optimal convolutional approximate message-passing (CAMP) for signal recovery in compressed sensing. CAMP uses the same low-complexity matched filter (MF) for interference suppression as approximate message-passing…
A modification of the Adaptive Biasing Force method is introduced, in which the free energy is approximated by a sum of tensor products of one-dimensional functions. This enables to handle a larger number of reaction coordinates than the…
The essential features of far-field low-energy defibrillation are elucidated using a simple cellular automaton model of excitable media. The model's topological character allows for direct correspondence with both realistic models and…
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…
Machine-learned interatomic potentials (MLPs) provide near density functional theory (DFT) accuracy at reduced computational cost, but their reliability depends on representative training data and often deteriorates in transition-state…
Road vehicles contribute to significant levels of greenhouse gas (GHG) emissions. A potential strategy for improving their aerodynamic efficiency and reducing emissions is through active adaptation of their exterior shapes to the…
We study motor traffic on Bethe networks subject to hard-core exclusion for both tightly coupled one-state machines and loosely coupled two-state machines that perform work against a constant load. In both cases we find an…
The accelerated proximal point algorithm (APPA), also known as "Catalyst", is a well-established reduction from convex optimization to approximate proximal point computation (i.e., regularized minimization). This reduction is conceptually…
We calculate a current rectification by molecules containing a conjugated molecular group sandwiched between two saturated (insulating) molecular groups of different length (molecular quantum dot) using an ab-initio non-equilibrium Green's…
In eukaryotic cells, many motor proteins can move simultaneously on a single microtubule track. This leads to interesting collective phenomena like jamming. Recently we reported ({\it Phys. Rev. Lett. {\bf 95}, 118101 (2005)}) a lattice-gas…