Session Z42: Focus Session: Physics of Biomaterials: Mechanics, Dynamics, and Transport

Highly parallel computational study of amphiphilic molecules using the Wang--Landau method

The self-assembly process in amphiphilic solutions is a phenomenon of broad interest. Molecular dynamics simulations generally used to study micelle formation or lipid layer assembly in an explicit solvent are limited in time scale. Vast studies of structure formation processes via standard Markov-chain based Monte Carlo simulations are challenging, but the Wang--Landau method~[1] provides a way to efficiently study such systems in a generalized thermodynamic ensemble. This makes it possible, for example, to get results over a broad temperature range from a single simulation. In an attempt to develop highly parallel applications using this method, we study the thermodynamic behavior of a generic coarse-grained model for amphiphilic molecules~[2] as well as of a new coarse-grained lipid model specifically designed for dimyristoyl phosphatidylcholine (DMPC)~[3]. Here, we focus on the design and the performance of our parallel Wang--Landau simulation on multi-CPU and GPU systems.\\[4pt] [1] F. Wang and D.P. Landau, Phys. Rev. Lett. \textbf{86}, 2050 (2001)\\[0pt] [2] S. Fujiwara et al., J. Chem. Phys. \textbf{130}, 144901 (2009)\\[0pt] [3] W. Shinoda et al., J. Phys. Chem. B \textbf{114}, 6836 (2010)   

Spatial response variations within biosensor flow cells

Biosensors are currently being developed for the detection of a wide range of analytes in a variety of scenarios. One such area is that of environmental monitoring for the presence of biological threats, from toxins through to viruses and bacteria. The varying nature, and in particular disparate size, of such a variety of analytes poses a significant challenge in the development of effective high confidence instruments. Many existing biosensors employ functionalised flow cells in which spatially defined arrays of surface immobilised recognition elements are present to specifically capture their analyte of interest. Experimental data obtained using a grating coupled SPR instrument, the BIAcore{\texttrademark} Flexchip, has revealed spatial dependency differences in response behaviours between proteinaceous and particulate analytes. In particular, the magnitude of responses seen with \textit{Bacillus anthracis} spores across the instruments flow cell appear to be influenced by shear and gravitational effects whilst those from soluble proteins are more uniform. We have explored this dependence to understand its fundamental impact on the successful implementation of multi-analyte environmental biological detection systems.   

Size-dependent mechanical properties of low-dimensional materials: coupling between deformation modes

Coupling between deformation modes, such as tension, bending, shear, and twisting, are widely observed in low-dimensional materials, especially biological materials. In this talk we will present our study on microtubules (MT) mechanics, where significance of mode coupling leads remarkable size-dependence in structural and mechanical properties. Using molecular dynamics (MD) simulations, we find a distinct dependence of bending rigidity on the contour length of a MT that agrees well with experimental data. We develop a simple model by including basic parameters to explain and predict this interesting phenomenon. An extended discussion will be made to general low-dimensional materials, with focuses not only on the mechanism, but also applications in optimal materials design.   

A QM/MM method for simulating the sequencing of DNA using graphene nanopores: solvent efects on nucleobase selectivity

The possibility of using graphene nanopores for DNA sequencing is driving a significant research effort with the aim of obtaining cheaper, more efficient, sequencing techniques. In this work we will present electronic transport calculations of graphene nanopores used for sequencing DNA strands. We consider both single layer and double layer graphene with different types of functionalization of the pore edges. The simulations were performed using a QM/MM method which allows us to treat the graphene sheet containing the nanopore and a segment of DNA within the pore via ab initio DFT methods (QM) whereas the effects of the water molecules, the counter-ions and the remainder of the DNA strand is taken into consideration using a classical potential (MM). The electronic transport properties along graphene are subsequently calculated using non-equilibrium Green's functions including the classical potential. Different time steps of classical molecular dynamics simulations of the DNA strand passing through the nanopore are considered in order to simulate the translocation process. This way we are able to address the effects of the solvent on the selectivity of the device to different nucleobases using atomistic methods.   

First-Principles Study of Muon Trapping in Singlet and Triplet States of Oxyhemoglobin

There is great current interest in the possibility of magnetic character in oxyhemoglobin (OxyHb) due to the detection [1] of muon spin-lattice relaxation in OxyHb. First-Principles variational Hartree-Fock Many Body Perturbation Theory (VHFMBPT) technique investigations on the singlet and triplet states of pure OxyHb have shown$^{2}$ that the triplet state is considerably higher than the singlet state ruling out magnetic character. However the charge distribution obtained by the VHFMBPT procedure in both states show a number of sites that have negative charges where the trapping of muon is being investigated to examine if the energy gap in the ordering of singlet and triplet states can be reduced or reversed leading to magnetic effects. Other possible sources of magnetism in Oxyhemoglobin will also be discussed. 1. K. Nagamine et al. Proc. Japan. Acad. B-Physics 83, 120 (2007); 2. S.R. Badu et al. Reported at Third Joint HFI-NQI International Conference, CERN, Geneva, September 2010.   

Branched Polymer Models and the Mechanism of Multilayer Film Buildup

The ``in and out diffusion'' hypothesis does not provide a sufficient explanation of the exponential buildup displayed by some polyelectrolyte multilayer film systems. Here, we report initial tests of an alternative view, on which the completion of each adsorption cycle results in an increase in the number of polymer binding sites on the film surface. Polycationic dendrimeric peptides, which can potentially bind several oppositely-charged peptides each, have been designed, synthesized and utilized in comparative film buildup experiments. Material deposited, internal film structure and film surface morphology have been studied by ultraviolet spectroscopy (UVS), circular dichroism spectroscopy (CD), quartz crystal microbalance (QCM) and atomic force microscopy (AFM). Polycations tended to contribute more to film buildup than did polyanions on quartz but not on gold. Increasing the number of branches in the dendrimeric peptides from 4 to 8 reproducibly resulted in an increase in the film growth rate on quartz but not on gold. Peptide backbones tended to adopt a $\beta $-strand conformation on incorporation into a film. Thicker films had a greater surface roughness than thin films. The data are consistent with film buildup models in which the average number of polymer binding sites will increase with each successive adsorption cycle in the range where exponential growth is displayed.   

Reduction of Scattered Light by M\"uller Cells in the Human Retina

It is a long standing question why in the mammalian eye photoreceptors are positioned at the back of the retina, forcing photons to travel through various neuronal layers of the retina before the light-sensitive rods and cones can detect them. Recent studies suggest that certain retinal glial cells--called M\"uller cells (MCs)--play an important role in answering that question. It has been experimentally shown that MCs extracted from the retina can act as optical fibers [1]. To understand the light guiding properties of the MC in the natural fluctuating optical environment, we developed a model to analyze the light reflection and transmission of MCs embedded in a random medium neuronal tissue. With these quantities and a simplified geometrical eye model we study how light is scattered in the eye. We found that MCs can lead to a substantial increase of the signal-to-noise ratio (SNR), the ratio of the intensity of direct incident light at a photoreceptor to the intensity of back-scattered light from other areas of the retina. The SNR is most pronounced in the vicinity of the fovea and can be more than an order of magnitude.\\[4pt] [1] Franze et. al., Proc Natl Acad Sci USA, 2007, 104, 8287-8292.   

Quantifying the deformation of the red blood cell skeleton in shear flow

To quantitatively predict the response of red blood cell (RBC) membrane in shear flow, we carried out multiphysics simulations by coupling a three-level multiscale approach of RBC membranes with a Boundary Element Method (BEM) for surrounding flows. Our multiscale approach includes a model of spectrins with the domain unfolding feature, a molecular-based model of the junctional complex with detailed protein connectivity and a whole cell Finite Element Method (FEM) model with the bilayer-skeleton friction derived from measured transmembrane protein diffusivity based on the Einstein-Stokes relation. Applying this approach, we investigated the bilayer-skeleton slip and skeleton deformation of healthy RBCs and RBCs with hereditary spherocytosis anemia during tank-treading motion. Compared with healthy cells, cells with hereditary spherocytosis anemia sustain much larger skeleton-bilayer slip and area deformation of the skeleton due to deficiency of transmembrane proteins. This leads to extremely low skeleton density and large bilayer-skeleton interaction force, both of which may cause bilayer loss. This finding suggests a possible mechanism of the development of hereditary spherocytosis anemia.   

Theoretical study of electron transport in DNA

Multiple experiments have indicated high conductivity of DNA, but its origin has not yet been satisfactorily explained. In this work, we explore the conductivity of double stranded B-DNA using a nonequilibrium Green's function method based on density-functional theory. The DNA is sandwiched between metallic nanotube leads and we investigate the effect of various linkers connecting the DNA to the leads. Our results show that the alkane linker, $(CH_2)_n$, which is often used in experiments, dramatically decreases the conductivity due to its large band gap around the Fermi level. We also find that conductivity can be greatly enhanced by aligning the highest occupied molecule orbital energy of DNA with the Fermi level of the leads by applying a gate bias to the DNA. Finally, we examine the effects of misalignment and mismatches on conductivity of DNA.