Specific heat and partition function zeros for the dimer model on the checkerboard B lattice: Finite-size effects.

There are three possible classifications of the dimer weights on the bonds of the checkerboard lattice and they are denoted as checkerboard A, B, and C lattices [Phys. Rev. E 91, 062139 (2015)PLEEE81539-375510.

Finite-size corrections and scaling for the dimer model on the checkerboard lattice.

Lattice models are useful for understanding behaviors of interacting complex many-body systems. The lattice dimer model has been proposed to study the adsorption of diatomic molecules on a substrate. Here we analyze the partition function of the dimer model on a 2M×2N checkerboard lattice wrapped on a torus and derive the exact asymptotic expansion of the logarithm of the partition function.

Disorder profile of nebulin encodes a vernierlike position sensor for the sliding thin and thick filaments of the skeletal muscle sarcomere.

Nebulin is an about 1μm long intrinsically disordered scaffold for the thin filaments of skeletal muscle sarcomere. It is a multifunctional elastic protein that wraps around actin filament, stabilizes thin filaments, and regulates Ca-dependent actomyosin interactions. This study investigates whether the disorder profile of nebulin might encode guidelines for thin and thick filament interactions in the sarcomere of the skeletal muscle.

Surface electromyography analysis of blepharoptosis correction by transconjunctival incisions.

Upper eyelid movement depends on the antagonistic actions of orbicularis oculi muscle and levator aponeurosis. Blepharoptosis is an abnormal drooping of upper eyelid margin with the eye in primary position of gaze. Transconjunctival incisions for upper eyelid ptosis correction have been a well-developed technique.

Simplified lattice model for polypeptide fibrillar transitions.

Polypeptide fibrillar transitions are studied using a simplified lattice model, modified from the three-state Potts model, where uniform residues as spins, placed on a cubic lattice, can interact with neighbors to form coil, helical, sheet, or fibrillar structure. Using the transfer matrix method and numerical calculations, we analyzed the partition function and construct phase diagrams. The model manifests phase transitions among coil, helix, sheet, and fibril through parameterizing bond coupling energy ɛh,ɛs,ɛf, structural entropies sh,ss,sf of helical, sheet, and fibrillar states, and number density ρ.

The role of tryptophan in staphylococcal nuclease stability.

Staphylococcal nuclease (SNase) has a single Trp residue at position 140. Circular dichroism, intrinsic and ANS-binding fluorescence, chemical titrations and enzymatic assays were used to measure the changes of its structure, stability and activities as the Trp was mutated or replaced to other positions. The results show that W140 is critical to SNase structure, stability, and function.

Phase statistics approach to human ventricular fibrillation.

Ventricular fibrillation (VF) is known to be the most dangerous cardiac arrhythmia, frequently leading to sudden cardiac death (SCD). During VF, cardiac output drops to nil and, unless the fibrillation is promptly halted, death usually ensues within minutes. While delivering life saving electrical shocks is a method of preventing SCD, it has been recognized that some, though not many, VF episodes are self-terminating, and understanding the mechanism of spontaneous defibrillation might provide newer therapeutic options for treatment of this otherwise fatal arrhythmia.

Thermostability of the N-terminal RNA-binding domain of the SARS-CoV nucleocapsid protein: experiments and numerical simulations.

Differential scanning calorimetry, circular dichroism spectroscopy, nuclear magnetic resonance spectroscopy, and numerical simulations were used to study the thermostability of the N-terminal RNA-binding domain (RBD) of the SARS-CoV nucleocapsid protein. The transition temperature of the RBD in a mixing buffer, composed of glycine, sodium acetate, and sodium phosphate with 100 mM sodium chloride, at pH 6.8, determined by differential scanning calorimetry and circular dichroism, is 48.

Multiple nucleic acid binding sites and intrinsic disorder of severe acute respiratory syndrome coronavirus nucleocapsid protein: implications for ribonucleocapsid protein packaging.

The nucleocapsid protein (N) of the severe acute respiratory syndrome coronavirus (SARS-CoV) packages the viral genomic RNA and is crucial for viability. However, the RNA-binding mechanism is poorly understood. We have shown previously that the N protein contains two structural domains--the N-terminal domain (NTD; residues 45 to 181) and the C-terminal dimerization domain (CTD; residues 248 to 365)--flanked by long stretches of disordered regions accounting for almost half of the entire sequence.

Enveloping triangulation method for detecting internal cavities in proteins and algorithm for computing their surface areas and volumes.

Detection and quantitative characterization of the internal cavities in proteins remain an important topic in studying protein structure and function. Here we propose a new analytical method for detecting the existence of cavities in proteins. The method is based on constructing the special enveloping triangulation enclosing the cavities.

Hydrophobic condensation and modular assembly model of protein folding.

Despite several decades of intense study, protein folding problem remains elusive. In this paper, we review current knowledge and the prevailing thinking in the field, and summarize our work on the in vitro folding of a typical small globular protein, staphylococcal nuclease (SNase). Various thermodynamic and kinetic methods have been employed to determine the energetic and construct the energy landscape of folding.

Compact dimension of denatured states of staphylococcal nuclease.

Fluorescence and circular dichroism stopped-flow have been widely used to determine the kinetics of protein folding including folding rates and possible folding pathways. Yet, these measurements are not able to provide spatial information of protein folding/unfolding. Especially, conformations of denatured states cannot be elaborated in detail.

Empirical mode decomposition and synchrogram approach to cardiorespiratory synchronization.

We use the empirical mode decomposition method to decompose experimental respiratory signals into a set of intrinsic mode functions (IMFs), and consider one of these IMFs as a respiratory rhythm. We then use the Hilbert spectral analysis to calculate the instantaneous phase of the IMF. Heartbeat data are finally incorporated to construct the cardiorespiratory synchrogram, which is a visual tool for inspecting synchronization.

Exact finite-size scaling functions for the interfacial tensions of the Ising model on planar lattices.

Exact finite-size scaling functions of the interfacial tensions are obtained for the Ising model with isotropic coupling on a set of M x N planar lattices, including square (sq), plane triangular (pt), and honeycomb (hc) lattices. The analyses of transitive behaviors at criticality revise the knowledge of the interfacial tensions as a function of the aspect ratio defined by R = M/N for R approaching to zero gradually. The amplitudes of the interfacial tensions for the sq, pt, and hc lattices are further shown to have relative proportions 1:square root of 3 / 2:square root of 3 which are related to the aspect ratios for the three lattices to have similar domains.

Finite-size corrections and scaling for the triangular lattice dimer model with periodic boundary conditions.

We analyze the partition function of the dimer model on M x N triangular lattice wrapped on the torus obtained by Fendley, Moessner, and Sondhi [Phys. Rev. B 66, 214513, (2002)].

Phase distribution and phase correlation of financial time series.

The scaling, phase distribution, and phase correlation of financial time series are investigated based on the Dow Jones Industry Average and NASDAQ 10-min intraday data for a period from 1 Aug. 1997 to 31 Dec. 2003.

Universal finite-size scaling functions with exact nonuniversal metric factors.

Using exact partition functions and finite-size corrections for the Ising model on finite square, plane triangular, and honeycomb lattices and extending a method [J. Phys. 19, L1215 (1986)] to subtract leading singular terms from the free energy, we obtain universal finite-size scaling functions for the specific heat, internal energy, and free energy of the Ising model on these lattices with exact nonuniversal metric factors.

Unzipping of DNA with correlated base sequence.

We consider force-induced unzipping transition for a heterogeneous DNA model with a correlated base sequence. Both finite-range and long-range correlated situations are considered. It is shown that finite-range correlations increase stability of DNA with respect to the external unzipping force.