First, in order to use as an inlet condition for turbulent simulation, a method is presented which produces numerically an artificial turbulence, namely, a series of velocity fluctuations of which frequency is Gaussian, and energy spectrum and root mean square correspond to the given ones. Besides, the fluctuation data are determined by the characteristic parameters of turbulent flows such as t...

Motivated by the dynamics of a membrane in response to an external force, we study the thermally activated crossing of a semiflexible ring polymer over a potential barrier. For the bistable potential of Kramers type smoothly varying over a long length scale, we calculate the crossing rate using the multidimensional Kramers' rate theory and the functional integral method. We find that, due to it...

Residual fluctuations produced in typical experimental methodologies are examined as correlated noises. The effective range of the correlations was assessed by determining whether the decay over look-back time is better described as a power law or exponential. Both of these decay laws contain free parameters and it is argued that it is not possible to distinguish their models on the basis of si...

A finite-difference time-domain formalism for simulating coherent linear pulse propagation is presented that incorporates a medium response described by any two-time energy gap correlation function. Two algorithms, for real and complex correlation functions, are developed to evaluate the electric polarization through explicit treatment of the density matrix for a two-level system. The coherence...

Real option analysis (ROA) is a way of valuing real assets by invoking option pricing theory. In contrast to the traditional net present value approach, ROA makes it possible to explicitly incorporating management flexibility. Because of such advantages, ROA has become an important tool for project valuation and is widely used in practice. In this paper, we develop a real option model with regi...

Existing elastic network models are typically parametrized at a given cutoff distance and often fail to properly predict the thermal fluctuation of many macromolecules that involve multiple characteristic length scales. We introduce a multiscale flexibility-rigidity index (mFRI) method to resolve this problem. The proposed mFRI utilizes two or three correlation kernels parametrized at different...

Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which evolve by selectively rewiring links towards enhancing adaptability to a changing environment and stability against dynamical perturbations. We find that spars...

The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model-based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics--a classical simulation approach. The simulation method has been validated on a large set of molecular d...

In advanced-stage Parkinson's disease (PD), motor fluctuation is a frequent and disabling problem. Assessment of motor fluctuation depends on patient's subjective self-statement. We examined whether the subjective fluctuation matched the objective motor fluctuation defined by gait disorders. Using a new device, the portable gait rhythmogram, we recorded gait cadence and acceleration continuousl...