Lepton masses and mixing angles from heterotic orbifold models

We systematically study the possibility for realizing realistic values of lepton mass ratios and mixing angles by using only renormalizable Yukawa couplings derived from heterotic $Z_6$-I orbifold. We assume one pair of up and down sector Higgs fields. We consider both the Dirac neutrino mass scenario and the seesaw scenario with degenerate right-handed majorana neutrino masses. It is found that realistic values of the charged lepton mass ratios, $m_e/m_\tau$ and $m_\mu/m_\tau$, the neutrino mass squared difference ratio, $\Delta m^2_{31}/\Delta m^2_{21}$, and the lepton mixing angles can be obtained in certain cases.Comment: 22 pages, late

Capturing the essence of folding and functions of biomolecules using Coarse-Grained Models

The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such diverse length, and also time scales, requires models that capture the underlying physics for the particular length scale of interest. Theoretical ideas, in particular, concepts from polymer physics, have guided the development of coarse-grained models to study folding of DNA, RNA, and proteins. More recently, such models and their variants have been applied to the functions of biological nanomachines. Simulations using coarse-grained models are now poised to address a wide range of problems in biology.Comment: 37 pages, 8 figure

Measuring the energy landscape roughness and the transition state location of biomolecules using single molecule mechanical unfolding experiments

Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the energy landscape characteristics it is necessary to combine the experimental measurements with sound theoretical models and simulations. Here, we show how by using temperature as a variable in mechanical unfolding of biomolecules in laser optical tweezer or AFM experiments the roughness of the energy landscape can be measured without making any assumptions about the underlying reaction oordinate. The efficacy of the formalism is illustrated by reviewing experimental results that have directly measured roughness in a protein-protein complex. The roughness model can also be used to interpret experiments on forced-unfolding of proteins in which temperature is varied. Estimates of other aspects of the energy landscape such as free energy barriers or the transition state (TS) locations could depend on the precise model used to analyze the experimental data. We illustrate the inherent difficulties in obtaining the transition state location from loading rate or force-dependent unfolding rates. Because the transition state moves as the force or the loading rate is varied it is in general difficult to invert the experimental data unless the curvature at the top of the one dimensional free energy profile is large, i.e the barrier is sharp. The independence of the TS location on force holds good only for brittle or hard biomolecules whereas the TS location changes considerably if the molecule is soft or plastic. We also comment on the usefulness of extension of the molecule as a surrogate reaction coordinate especially in the context of force-quench refolding of proteins and RNA.Comment: 44 pages, 7 figure

Two-Dimensional Magnetic Resonance Tomographic Microscopy using Ferromagnetic Probes

We introduce the concept of computerized tomographic microscopy in magnetic resonance imaging using the magnetic fields and field gradients from a ferromagnetic probe. We investigate a configuration where a two-dimensional sample is under the influence of a large static polarizing field, a small perpendicular radio-frequency field, and a magnetic field from a ferromagnetic sphere. We demonstrate that, despite the non-uniform and non-linear nature of the fields from a microscopic magnetic sphere, the concepts of computerized tomography can be applied to obtain proper image reconstruction from the original spectral data by sequentially varying the relative sample-sphere angular orientation. The analysis shows that the recent proposal for atomic resolution magnetic resonance imaging of discrete periodic crystal lattice planes using ferromagnetic probes can also be extended to two-dimensional imaging of non-crystalline samples with resolution ranging from micrometer to Angstrom scales.Comment: 9 pages, 11 figure

Auger-assisted electron transfer from photoexcited semiconductor quantum dots

Although quantum confined nanomaterials, such as quantum dots (QDs) have emerged as a new class of light harvesting and charge separation materials for solar energy conversion, theoretical models for describing photoinduced charge transfer from these materials remain unclear. In this paper, we show that the rate of photoinduced electron transfer from QDs (CdS, CdSe, and CdTe) to molecular acceptors (anthraquinone, methylviologen, and methylene blue) increases at decreasing QD size (and increasing driving force), showing a lack of Marcus inverted regime behavior over an apparent driving force range of ∼0-1.3 V. We account for this unusual driving force dependence by proposing an Auger-assisted electron transfer model in which the transfer of the electron can be coupled to the excitation of the hole, circumventing the unfavorable Franck-Condon overlap in the Marcus inverted regime. This model is supported by computational studies of electron transfer and trapping processes in model QD-acceptor complexes

Extended hydrodynamics from Enskog's equation for a two-dimensional system general formalism

Balance equations are derived from Enskog's kinetic equation for a two-dimensional system of hard disks using Grad's moment expansion method. This set of equations constitute an extended hydrodynamics for moderately dense bi-dimensional fluids. The set of independent hydrodynamic fields in the present formulations are: density, velocity, temperature {\em and also}--following Grad's original idea--the symmetric and traceless pressure tensor $p_{ij}$ and the heat flux vector $\mathbf q^{k}$. An approximation scheme similar in spirit to one made by Grad in his original work is made. Once the hydrodynamics is derived it is used to discuss the nature of a simple one-dimensional heat conduction problem. It is shown that, not too far from equilibrium, the nonequilibrium pressure in this case only depends on the density, temperature and heat flux vector.Comment: :9 pages, 1 figure, This will appear in J. Stat. Phys. with minor corrections and corresponds to Ref[9] of cond-mat/050710

Modelling the unfolding pathway of biomolecules: theoretical approach and experimental prospect

We analyse the unfolding pathway of biomolecules comprising several independent modules in pulling experiments. In a recently proposed model, a critical velocity $v_{c}$ has been predicted, such that for pulling speeds $v>v_{c}$ it is the module at the pulled end that opens first, whereas for $v<v_{c}$ it is the weakest. Here, we introduce a variant of the model that is closer to the experimental setup, and discuss the robustness of the emergence of the critical velocity and of its dependence on the model parameters. We also propose a possible experiment to test the theoretical predictions of the model, which seems feasible with state-of-art molecular engineering techniques.Comment: Accepted contribution for the Springer Book "Coupled Mathematical Models for Physical and Biological Nanoscale Systems and Their Applications" (proceedings of the BIRS CMM16 Workshop held in Banff, Canada, August 2016), 16 pages, 6 figure

Crowding Promotes the Switch from Hairpin to Pseudoknot Conformation in Human Telomerase RNA

Formation of a pseudoknot in the conserved RNA core domain in the ribonucleoprotein human telomerase is required for function. In vitro experiments show that the pseudoknot (PK) is in equilibrium with an extended hairpin (HP) structure. We use molecular simulations of a coarse-grained model, which reproduces most of the salient features of the experimental melting profiles of PK and HP, to show that crowding enhances the stability of PK relative to HP in the wild type and in a mutant associated with dyskeratosis congenita. In monodisperse suspensions, small crowding particles increase the stability of compact structures to a greater extent than larger crowders. If the sizes of crowders in a binary mixture are smaller than the unfolded RNA, the increase in melting temperature due to the two components is additive. In a ternary mixture of crowders that are larger than the unfolded RNA, which mimics the composition of ribosome, large enzyme complexes and proteins in E. coli, the marginal increase in stability is entirely determined by the smallest component. We predict that crowding can restore partially telomerase activity in mutants, which dramatically decrease the PK stability.Comment: File "JACS_MAIN_archive_PDF_from_DOC.pdf" (PDF created from DOC) contains the main text of the paper File JACS_SI_archive.tex + 7 figures are the supplementary inf

Role of quantum coherence in chromophoric energy transport

The role of quantum coherence and the environment in the dynamics of excitation energy transfer is not fully understood. In this work, we introduce the concept of dynamical contributions of various physical processes to the energy transfer efficiency. We develop two complementary approaches, based on a Green's function method and energy transfer susceptibilities, and quantify the importance of the Hamiltonian evolution, phonon-induced decoherence, and spatial relaxation pathways. We investigate the Fenna-Matthews-Olson protein complex, where we find a contribution of coherent dynamics of about 10% and of relaxation of 80%.Comment: 5 pages, 3 figures, included static disorder, correlated environmen