Alignment of molecules in pulsed resonant laser fields

We investigate by numerical simulations the dynamics of alignment of linear molecules in resonant pulsed laser fields and its dependence on pulse length, field strength, and molecular parameters. We propose an analytical short-time approximation for the time-dependent wave packets. We provide a theoretical basis for the occurrence of saturation in the rotational pumping. We present a formula to predict the time at which the maximum alignment occurs. We discuss the magnitude of the laser-induced alignment and we relate it to a theoretical upper limit.     

Self-assembly of magnetic nanostructures

We use Monte Carlo and quaternion molecular dynamics simulations to study the self-assembly of intriguing structures which form in colloidal suspensions of small magnetite particles. We show that the only stable isomers with few particles, a ring and a chain, can be efficiently interconverted using a magnetizable tip. We propose to use the oscillating dipole field of the tip to locally anneal the aggregates to either a ring in zero field or a chain in nonzero applied field.     

Coil-stretch Transition of DNA Molecules in Slit-like Confinement

We experimentally investigate the influence of slit-like confinement on the coil-stretch transition of single DNA molecules in a homogeneous planar elongational electric field. We observe a more gradual coil-stretch transition characterized by two distinct critical strain rates for DNA in confinement, different from the unconfined case where a single critical strain rate exists. We postulate that the change in the coil-stretch transition is due to a modified spring law in confinement. We develop a dumbbell model to extract an effective spring law by following the relaxation of an initially stretched DNA. We then use this spring law and kinetic theory modeling to predict the extension and fluctuations of DNA in planar elongational fields. The model predicts that a two-stage coil-stretch transition emerges in confinement, in accord with experimental observations.     

Temperature dependence of the fluorescence properties of curcumin

Steady-state and time-resolved techniques were employed to study the nonradiative process of curcumin dissolved in ethanol and 1-propanol in a wide range of temperatures. We found that the nonradiative rate constants at temperatures between 175-250 K qualitatively follow the same trend as the dielectric relaxation times of both neat solvents. We attribute the nonradiative process to solvent-controlled proton transfer. We also found a kinetic isotope effect on the nonradiative process rate constant of ~2. We propose a model in which the excited-state proton transfer breaks the planar hexagonal structure of the keto-enol center of the molecule. This, in turn, enhances the nonradiative process driven by the twist angle between the two phenol moieties.     

Statistical Inference of Distribution of Crystal Size by X-Ray Powder Diffraction

We describe a method to calculate the distribution of sizes of fine crystals from pure powder-diffraction profile using a method of maximum entropy (MAXENT). We apply a Monte-Carlo technique of simulated annealing to seek a global minimum of the error surface in fitting this diffraction profile. We consider pure diffraction profile (instrument de-convoluted) of a powder specimen without lattice imperfection to a significant extent. Under these circumstances, the distribution of the pure diffraction profile can be attributed to the distribution of crystallite size. We applied this method to three cases of crystal sizes having a highly inhomogeneous distribution with certain noise-tolerance. The results agree well with synthetic data of diffraction.     

Analyzing mechanisms and microscopic reversibility of self-assembly

We use computer simulations to investigate self-assembly in a system of model chaperonin proteins, and in an Ising lattice gas. We discuss the mechanisms responsible for rapid and efficient assembly in these systems, and we use measurements of dynamical activity and assembly progress to compare their propensities for kinetic trapping. We use the analytic solution of a simple minimal model to illustrate the key features associated with such trapping, paying particular attention to the number of ways that particles can misbind. We discuss the relevance of our results for the design and control of self-assembly in general.     

Effect of cosurfactant on the free-drainage regime of aqueous foams

We report results of drainage in aqueous foams of small bubble size D (D=180 microm) prepared with SDS-dodecanol solutions. We have performed free-drainage experiments in which local drainage rates are measured by electrical conductivity and by light scattering techniques. We have investigated the role of the surfactant-cosurfactant mass ratio on the drainage regime. The results confirm that a drainage regime corresponding to a high surface mobility can indeed be found for such small bubbles, and show that an increase in the cosurfactant content can induce a transition to a low surface mobility drainage regime. We show that the transition is not linked to variations of the bulk properties, but rather to variations of the interfacial properties. However, the results show that the added amount of dodecanol to trigger the transition is quite high, evidencing that the relevant control parameter for drainage regimes includes both bubble size and interfacial contributions.     

On the Helical Crystals of Cholesterol Monohydrate

We review in this short perspective the history of cholesterol crystals and crystal structures. We address in particular the helical crystals that form in vitro and in pathology from environments rich in bile acids or from phospholipid membranes. We review the known mechanisms leading to crystals with chiral morphology, from screw-dislocation mediated growth to mechanisms involving asymmetric mechanical strain. We propose a mechanism for cholesterol helical crystal development based on the monoclinic cholesterol monohydrate crystal structure. We suggest that curvature arises in few layers thick crystals due to the tension induced between the hydrophobic layer and the ice-like H-bonded lattice of the water molecules with the cholesterol hydroxy groups. Helicity would ensue through a combination of the curvature and the fast growth of a thin ribbon in one crystal direction.     

Langevin dynamics simulations of ds-DNA translocation through synthetic nanopores

We have implemented a coarse-grained model to study voltage-driven as-DNA translocation through nanopores located in synthetic membranes. The simulated trajectory of the DNA through the nanopores was calculated using Langevin dynamics. We present the results based on more than 120,000 individual translocations. We are particularly interested in this work in probing the physical basis of various experimentally observed--yet poorly understood--phenomena. Notably, we observe in our simulations the formation of ds-DNA hairpins, widely suspected to be the basis for quantized blockage. We study the translocation time, a measurable quantity crucially important in polyelectrolyte characterization, as a function of hairpin vertex location along the polymer backbone, finding that this behavior can be tuned to some degree by simulation parameters. We also study the voltage dependence of the tendency of hairpins to serve as the initiators of translocation events. Surprisingly, we find that the resulting probability depends vitally upon whether the events counted are ultimately successful or not. Further details lead us to propose that failed attempts in experimental translocation studies may be more common--and deceptive--than is generally recognized. We find the time taken by successful single file translocations to be directly proportional to the ratio of chain length to the applied voltage. Finally, we address a common yet puzzling phenomenon in translocation experiments: translocation events in which the current through the pore is highly, yet incompletely, blocked. We present the findings that offer a new explanation for such events.     

Average band structure of smectic C* type random materials

We consider a Smectic C* type structure which exhibits alignment fluctuations which can be described by noise associated with both director angles. We take the propagation of axially incident electromagnetic waves, and from Maxwell equations, we establish the stochastic governing set of equations corresponding to optical phenomena. We note that this set of equations can be expressed as a linear vector stochastic system of differential equations with multiplicative noise. We use a procedure to calculate from the stochastic differential set of equations, the governing equations for the expected value of the electromagnetic transverse magnetic and electric fields for a certain autocorrelation function, and calculate explicitly their corresponding band structure for a particular spectral noise density. We have shown that the average resulting electromagnetic fields exhibit a biased decaying exponential dependence which impedes to propagate the waves in one sense while it permits them in the other sense. We have also found a remarkable widening of the band gap and the appearance of new local maxima for the modes without band gap.     

Efficient quantification of the importance of contacts for the dynamical stability of proteins

Understanding the stability of the native state and the dynamics of a protein is of great importance for all areas of biomolecular design. The efficient estimation of the influence of individual contacts between amino acids in a protein structure is a first step in the reengineering of a particular protein for technological or pharmacological purposes. At the same time, the functional annotation of molecular evolution can be facilitated by such insight. Here, we use a recently suggested, information theoretical measure in biomolecular design - the Kullback-Leibler-divergence - to quantify and therefore rank residue-residue contacts within proteins according to their overall contribution to the molecular mechanics. We implement this protocol on the basis of a reduced molecular model, which allows us to use a well-known lemma of linear algebra to speed up the computation. The increase in computational performance is around 10(1)- to 10(4)-fold. We applied the method to two proteins to illustrate the protocol and its results. We found that our method can reliably identify key residues in the molecular mechanics and the protein fold in comparison to well-known properties in the serine protease inhibitor. We found significant correlations to experimental results, e.g., dissociation constants and Φ values.     

Comparing the density of states of binary Lennard-Jones glasses in bulk and film

We used Wang-Landau density of states Monte Carlo to study a binary Lennard-Jones glass-forming mixture in bulk and films between noninteracting walls. Thermodynamic properties are calculated using two different ensembles and film data are compared with the bulk. Bulk properties are in good agreement with previous simulations. We confirm the formation of a glass using various properties, e.g., energy, heat capacity, and pressure with temperature. We find a change in slope in the energy per particle and pressure as a function of temperature. We do not find any defined crystal structure. A higher glass transition temperature is found for the film.     

The potential and flux landscape theory of evolution

We established the potential and flux landscape theory for evolution. We found explicitly the conventional Wright's gradient adaptive landscape based on the mean fitness is inadequate to describe the general evolutionary dynamics. We show the intrinsic potential as being Lyapunov function(monotonically decreasing in time) does exist and can define the adaptive landscape for general evolution dynamics for studying global stability. The driving force determining the dynamics can be decomposed into gradient of potential landscape and curl probability flux. Non-zero flux causes detailed balance breaking and measures how far the evolution from equilibrium state. The gradient of intrinsic potential and curl flux are perpendicular to each other in zero fluctuation limit resembling electric and magnetic forces on electrons. We quantified intrinsic energy, entropy and free energy of evolution and constructed non-equilibrium thermodynamics. The intrinsic non-equilibrium free energy is a Lyapunov function. Both intrinsic potential and free energy can be used to quantify the global stability and robustness of evolution. We investigated an example of three allele evolutionary dynamics with frequency dependent selection (detailed balance broken). We uncovered the underlying single, triple, and limit cycle attractor landscapes. We found quantitative criterions for stability through landscape topography. We also quantified evolution pathways and found paths do not follow potential gradient and are irreversible due to non-zero flux. We generalized the original Fisher's fundamental theorem to the general (i.e., frequency dependent selection) regime of evolution by linking the adaptive rate with not only genetic variance related to the potential but also the flux. We show there is an optimum potential where curl flux resulting from biotic interactions of individuals within a species or between species can sustain an endless evolution even if the physical environment is unchanged. We offer a theoretical basis for explaining the corresponding Red Queen hypothesis proposed by Van Valen. Our work provides a theoretical foundation for evolutionary dynamics.     

Monte Carlo analyses of multiple backscattering of gamma rays

We have written a Monte Carlo code to simulate the experimental results of a previously reported study. We were able to analyse the energy distributions of photons that reached the detector system after suffering several successive Compton scatterings in the target. We have also investigated how the number of multiply backscattered events depends on the target thickness and the energy of the primary photons.     

Double transfer printing of small volumes of liquids

We report here a technique to print small volumes of liquid on a hydrophobic substrate. This process is based on the control of the critical parameters that govern a quasi-equilibrium liquid transfer process from one surface to another. We present a qualitative model that describes the physics of a transfer printing process between hydrophobic surfaces, and we use the parameters outlined in this model to manipulate the amount of liquid transferred between surfaces. We demonstrate the printing of discrete, small volumes (approximately 70 fL) of different liquid inks on a polymer substrate starting with volumes that are 8 orders of magnitude larger (a droplet of approximately 10 microL) in a simple two-step procedure.     

Electrical detection of single methylcytosines in a DNA oligomer

We report label-free electrical detections of chemically modified nucleobases in a DNA using a nucleotide-sized electrode gap. We found that methyl substitution contributes to increase the tunneling conductance of deoxycytidines, which was attributed to a shift of the highest occupied molecular orbital level closer to the electrode Fermi level by methylation. We also demonstrate statistical identifications of methylcytosines in an oligonucleotide by tunneling current. This result suggests a possible use of the transverse electron-transport method for a methylation level analysis.     

Effect of Temperature and Inhomogeneities on Binding of a Ligand to Haeme Proteins

We apply a quantum-mechanical theory of rate processes to treat the recombination of ligands to haeme proteins such as myoglobin. Emphasis is placed on the effect of temperature in the low-temperature regime. We present a theory of time-resolved spectra pertaining to protein dynamics. We emphasize the analysis of the entire spectrum rather than spectral shifts as a function of time.     

Surface plasmon mapping of dumbbell-shaped gold nanorods: the effect of silver coating

We report on the identification of surface plasmons in individual gold dumbbell-shaped nanoparticles (AuDBs), as well as AuDBs coated with silver. We use spatially resolved electron energy-loss spectroscopy in a scanning electron microscope, which allows us to map plasmon-energy and intensity spatial distributions. Two dominant plasmon resonances are experimentally resolved in both AuDBs and silver-coated AuDBs. The intensity of these features is peaked either at the tips or at the sides of the nanoparticles. We present boundary element method simulations in good agreement with the experiment, allowing us to elucidate the nature of such modes. While the lower-energy, tip-focused plasmon is of longitudinal character for all dumbbells under consideration, the second side-bound plasmon has a more involved symmetry, starting as a longitudinal quadrupole in homogeneous AuDBs and picking up transversal components when silver coating is added. The longitudinal dipolar mode energy is found to blue-shift upon coating with silver. We find that the substrate produces sizable shifts in the plasmons of silver-coated AuDBs. Our analysis portraits a complex plasmonic scenario in metal nanoparticles coated with silver, including a transition from the original homogeneous gold dumbbell plasmons to the modes of homogeneous silver rods. We believe that these findings can have potential application to plasmon engineering.     

Site-selective bromination of vancomycin

We report the site-selective bromination of vancomycin to produce, with substantial efficiency, previously unknown monobromovancomycins, a dibromovancomycin, and a tribromovancomycin. We document the inherent reactivity of native vancomycin toward N-bromophthalimide. We then demonstrate significant rate acceleration and perturbation of the inherent product distribution in the presence of a rationally designed peptide-based promoter. Alternative site selectivity is observed as a function of solvent and replacement of the peptide with guanidine.