Correlation between the dynamics of hydrogen bonds and the local density reorganization in the protein hydration layer

An atomistic molecular dynamics simulation of the protein villin headpiece subdomain or HP-36 has been carried out with explicit water to explore the microscopic inhomogeneity of local density reorganization of the hydration layers of the three alpha-helical segments of the protein. The density reorganization of the hydration layer of helix-3 is found to occur faster than that for the hydration layers of the other two helices. It is noticed that such inhomogeneous density reorganization at the surface of different secondary structures exhibits excellent correlation with the microscopic dynamics of hydrogen bonds between the protein residues and the hydration water. Further, it is observed that the reorientation of water molecules involved in the formation and breaking of protein-water or water-water hydrogen bonds plays an important role in determining the dynamics of local density of the hydration layer. The faster density reorganization of the hydration layer of helix-3 is also consistent with the functionality of HP-36, as helix-3 contains several active site residues.     

Low-frequency vibrational spectrum of water in the hydration layer of a protein: a molecular dynamics simulation study

An atomistic molecular dynamics simulation has been carried out to understand the low-frequency intermolecular vibrational spectrum of water present in the hydration layer of the protein villin headpiece subdomain or HP-36. An attempt is made to explore how the heterogeneous rigidity of the hydration layers of different segments (three alpha helices) of the protein, strength of the protein-water hydrogen bonds, and their differential relaxation behavior influence the distribution of the intermolecular vibrational density of states of water in the hydration layers. The calculations revealed that compared to bulk water these bands are nonuniformly blue-shifted for water near the helices, the extent of shifts being more pronounced for water molecules hydrogen bonded to the protein residues. It is further noticed that the larger blue shift observed for the water molecules hydrogen bonded to helix 2 residues correlates excellently with the slowest structural relaxation of these hydrogen bonds. These results can be verified by suitable experimental measurements.     

Interaction of cinnamic acid derivatives with serum albumins: a fluorescence spectroscopic study

Cinnamic acid (CA) derivatives are known to possess broad therapeutic applications including anti-tumor activity. The present study was designed to determine the underlying mechanism and thermodynamic parameters for the binding of two CA based intramolecular charge transfer (ICT) fluorescent probes, namely, 4-(dimethylamino) cinnamic acid (DMACA) and trans-ethyl p-(dimethylamino) cinnamate (EDAC), with albumins by fluorescence spectroscopy. Stern-Volmer analysis of the tryptophan fluorescence quenching data in presence of the added ligand reveals fluorescence quenching constant (κ(q)), Stern-Volmer constant (K(SV)) and also the ligand-protein association constant (K(a)). The thermodynamic parameters like enthalpy (ΔH) and entropy (ΔS) change corresponding to the ligand binding process were also estimated. The results show that the ligands bind into the sub-domain IIA of the proteins in 1:1 stoichiometry with an apparent binding constant value in the range of 10(4) dm(3) mol(-1). In both the cases, the spontaneous ligand binding to the proteins occur through entropy driven mechanism, although the interaction of DMACA is relatively stronger in comparison with EDAC. The temperature dependence of the binding constant indicates the induced change in protein secondary structure.     

Real time disruption management for a two-stage batch production–inventory system with reliability considerations

In this research, a two-stage batch production–inventory system is introduced. In this system, the production may be disrupted, for a given period of time, either at one or both stages. In this paper, firstly, a mathematical model has been developed to suggest a recovery plan for a single occurrence of disruption at either stage. Secondly, multiple disruptions have been considered, for which a new disruption may or may not affect the recovery plan of earlier disruptions. We propose a new approach that deals with a series of disruptions over a period of time, which can be implemented for disruption recovery on a real time basis. In this approach, the model formulated for single disruption has been integrated to generate initial solutions for individual disruptions and the solutions have been revised for multiple dependent disruptions with changed parameters. With the proposed approach, an optimal recovery plan can be obtained in real time, whenever the production system experiences either a sudden disruption or a series of disruptions, at different points in time. Some numerical examples and a real-world case study are presented to explain the benefits of our proposed approach.     

Information entropic measures of a quantum harmonic oscillator in symmetric and asymmetric confinement within an impenetrable box

Information‐based uncertainty measures like Shannon entropy, Onicescu energy and Fisher information (in position and momentum space) are employed to understand the effect of symmetric and asymmetric confinement in a quantum harmonic oscillator. Also, the transformation of the Hamiltonian into a dimensionless form gives an idea of the composite effect of force constant and confinement length (x_c). In the symmetric case, a wide range of x_c has been taken up, whereas asymmetric confinement is dealt with by shifting the minimum of the potential from the origin keeping box length and boundary fixed. Eigenvalues and eigenvectors for these systems are obtained quite accurately via an imaginary‐time propagation scheme. For asymmetric confinement, a variation‐induced exact diagonalization procedure is also introduced, which produces very high quality results. One finds that, in symmetric confinement, after a certain characteristic x_c, all these properties converge to respective values of a free harmonic oscillator. In the asymmetric situation, excited‐state energies always pass through a maximum. For this potential, the classical turning point decreases, whereas well depth increases with the strength of asymmetry. A study of these uncertainty measures reveals that localization increases with an increase of the asymmetry parameter.

     

Hydrodynamic self-consistent field theory for inhomogeneous polymer melts

We introduce a mesoscale technique for simulating the structure and rheology of block-copolymer melts and blends in hydrodynamic flows. The technique couples dynamic self-consistent field theory with continuum hydrodynamics and flow penalization to simulate polymeric fluid flows in channels of arbitrary geometry. We demonstrate the method by studying phase separation of an ABC triblock copolymer melt in a submicron channel with neutral wall wetting conditions. We find that surface wetting effects and shear effects compete, producing wall-perpendicular lamellae in the absence of flow and wall-parallel lamellae in cases where the shear rate exceeds some critical Weissenberg number.     

Perturbation of phospholipid bilayer properties by ethanol at a high concentration

Atomistic molecular dynamics (MD) simulations have been carried out at 30 degrees C on a fully hydrated liquid crystalline lamellar phase of dimyrystoylphosphatidylcholine (DMPC) lipid bilayer with embedded ethanol molecules at 1:1 composition, as well as on the pure bilayer phase. The ethanol molecules are found to exhibit a preference to occupy regions near the upper part of the lipid acyl chains and the phosphocholine headgroups. The calculations revealed that the phosphocholine headgroup dipoles (P- --> N+) of the lipids prefer to orient more toward the aqueous layer in the presence of ethanol. It is noticed that the ethanol molecules modify the dynamic properties of both lipids as well as the water molecules in the hydration layer of the lipid headgroups. Both the in-plane "rattling" and out-of-plane "protrusion" motions of the lipids have been found to increase in the presence of ethanol. Most importantly, it is observed that the water molecules within the hydration layer of the lipid headgroups exhibit faster translational and rotational motions in the presence of ethanol. This arises due to faster dynamics of hydrogen bonds between lipid headgroups and water in the presence of ethanol.     

Coupling between hydration layer dynamics and unfolding kinetics of HP-36

We have performed atomistic molecular dynamics simulations of aqueous solutions of HP-36 at 300 K in its native state, as well as at high temperatures to explore the unfolding dynamics of the protein and its correlation with the motion of water around it. On increasing the temperature a partially unfolded molten globule state is formed where the smallest alpha helix (helix 2) unfolds into a coil. It is observed that the unfolding is initiated around the residue Phe-18 which shows a sharp displacement during unfolding. We have noticed that the unfolding of the protein affects the density of water near the protein surface. Besides, the dynamics of water in the protein hydration layer has been found to be strongly correlated with the time evolution of the unfolding process. We have introduced and calculated a displacement time correlation function to monitor the change in water motion relative to the protein backbone during unfolding. We find that the unfolding of helix 2 is associated with an increase in mobility of water around it as compared to water around the other two helices. We have also explored the microscopic aspects of secondary structure specific and site specific solvation dynamics of the protein. The calculations reveal that unfolding influences the solvation dynamics of the protein molecule in a heterogeneous manner depending on the location of the polar probe residues. This seems to be in agreement with recent experimental findings.     

Composite nonlinear feedback based discrete integral sliding mode controller for uncertain systems

In this paper, a discrete integral sliding mode (ISM) controller based on composite nonlinear feedback (CNF) method is proposed. The aim of the controller is to improve the transient performance of uncertain systems. The CNF based discrete ISM controller consists of a linear and a nonlinear term. The linear control law is used to decrease the damping ratio of the closed-loop system for yielding a quick transient response. The nonlinear feedback control law is used to increase the damping ratio with an aim to reduce the overshoot of the closed-loop system as it approaches the desired reference position. It is observed that the discrete CNF-ISM controller produces superior transient performance as compared to the discrete ISM controller. The closed-loop control system remains stable during the sliding condition. Simulation results demonstrate the effectiveness of the proposed controller.     

Synthesis and surface modified hard magnetic properties in Co0.5Pt0.5 nanocrystallites from a rheological liquid precursor

Small crystallites of a metastable phase Co_0.5Pt_0.5 are precipitated by heating a rheological liquid precursor of cobalt–hydrazine complex and platinum chloride H₂PtCl₆·xH₂O in polymer molecules of poly(vinylpyrrolidone) (PVP) in ethylene glycol. The hydrazine co-reduces nascent atoms from the Co²⁺ and Pt⁴⁺ that recombine and grow as Co_0.5Pt_0.5. The PVP molecules cap a growing Co_0.5Pt_0.5 as it achieves a critical size so that it stops growing further in given conditions. X-ray diffraction pattern of a recovered powder reveals a crystalline Co_0.5Pt_0.5 phase (average crystallite size D∼8 nm) of a well-known Fm3m-fcc crystal structure with the lattice parameter a=0.3916 nm (density ρ=14.09 g/cm³). A more ordered L1₀ phase (ρ=15.91 g/cm³) transforms (D≥25 nm) upon annealing the powder at temperature lesser than 700 °C (in vacuum). At room temperature, the virgin crystallites bear only a small saturation magnetization M_s=5.54 emu/g (D=8 nm) of a soft magnet and it hardly grows on bigger sizes (D≤31 nm) in a canted ferromagnetic structure. A rectangular hysteresis loop is markedly expanded on an optimally annealed L1₀ phase at 800 °C for 60 min, showing a surface modified coercivity H_c=7.781 kOe with remnant ratio M_r/M_s=0.5564, and M_s=39.75 emu/g. Crystallites self-assembled in an acicular shape tailor large H_c from ideal single domains and high magnetocrystalline anisotropy of a hard magnet L1₀ phase.