Browsing by Subject "molecular dynamics"

Now showing 1 - 9 of 9

Open Access
Controlled lateral and perpendicular motion of atoms on metal surfaces
(1994) Buldum, Alper
Nanoscale modification of matter has been the subject of interest. Recently, several experimental studies have demonstrated that by using a scanning tunneling microscope one can translate atoms on metal surfaces to a desired position. Furthermore, it has been shown that an atom between surface and tip can be transferred reversibly which results in bistable conductance. The controlled dynamics of adsorbed species has opened a new field of research. This thesis work provides a theoretical investigation of the controlled lateral and perpendicular motion of an inert gas atom (Xe) on metal surfaces. The lateral motion of Xe on the Ni(llO) and P t(lll) surfaces is manipulated by a W tip. The interaction energy of the physisorbed atom with the tip and metal surface is described by an empirical potential. Using molecular statics the energy surfaces are calculated and the adsorbtion sites are determined. By using the molecular dynamics calculations, the variation in the coordinates of the adsorbate Xe with the tip moving at a given height are obtained. Three different modes of Xe translation are distinguished depending on the height of the tip. These are i) carriage on the tip, ii) pushing and, iii) pulling modes. The range of the tip height where one of these modes occur is strongly depended on the relaxation of electrodes and the geometry of the tip. Controlled and reversible transfer of atoms between the metal surface and the tip is studied by the transfer of Xe between two flat P t(lll) surfaces. Physisorption of Xe on the P t(lll) surface is studied by an empirical potential including short and long-range interactions and yielding correct account of several experimental data. Effective charge on Xe and the dipole moment constructed therefrom are calculated as a function of the Xe-surface separation. The potential energy curve of Xe between two P t(lll) surfaces and quantum states of Xe therein are calculated as a function of the applied voltage and separation between two P t (lll) surfaces. Within this model, various mechanisms, such as tunneling of Xe, dipole excitation and resonant tunneling, electromigration contributing to the transfer of Xe are examined. The transfer rate of Xe is then calculated for different mechanisms. Its dependence on the bias voltage is explored. The overall behavior of the total transfer rate is not a power law. While at low bias voltages thermal assisted atom tunneling is effective, the dipole excitation and resonant tunneling becomes dominant at high bias voltages.
Open Access
Direct measurement of molecular stiffness and damping in confined water layers
(The American Physical Society, 2004) Jeffery, S.; Hoffmann, P. M.; Pethica, J. B.; Ramanujan, C.; Özer, H. Ö.; Oral, A.
We present direct and linear measurements of the normal stiffness and damping of a confined, few molecule thick water layer. The measurements were obtained by use of a small amplitude (0.36 Å), off-resonance atomic force microscopy technique. We measured stiffness and damping oscillations revealing up to seven molecular layers separated by 2.526 ± 0.482 Å. Relaxation times could also be calculated and were found to indicate a significant slow-down of the dynamics of the system as the confining separation was reduced. We found that the dynamics of the system is determined not only by the interfacial pressure, but more significantly by solvation effects which depend on the exact separation of tip and surface. The dynamic forces reflect the layering of the water molecules close to the mica surface and are enhanced when the tip-surface spacing is equivalent to an integer multiple of the size of the water molecules. We were able to model these results by starting from the simple assumption that the relaxation time depends linearly on the film stiffness.
Open Access
Electronic and atomic processes in nanowires
(1996) Mehrez, Hatem
The variation of conductance of a nanowire which is pulled between two metal electrodes has been the subject of dispute. Recent experimental set-ups using a combination of STM and AFM show that changes in conductivity are closely related with modification of atomic structure. In this thesis electron transport in the nanoindentation and in the connective neck are studied and features of measured conductance are analyzed. Molecular Dynamics simulations of nanowires under tensile stress are carried out to reveal the mechanical properties in nanowires in the course of stretching. A novel type of plcistic deformation, which leads to the formation of bundles with “giant” yield strength is found. An extensive analysis on how abrupt changes in the conductance and the last plateau before the break are related with “quantization phenomena” and atomic structure rearrangements in the neck. By using ab-initio self-consistent field pseudopotential calculations we also investigated electron properties of nanowires and atomic chains and predicted the large yield strength observed in the center of connective neck.
Open Access
Generation of phospholipid vesicle-nanotube networks and transport of molecules therein
(2011) Jesorka, A.; Stepanyants, N.; Zhang H.; Ortmen, B.; Hakonen, B.; Orwar O.
We describe micromanipulation and microinjection procedures for the fabrication of soft-matter networks consisting of lipid bilayer nanotubes and surface-immobilized vesicles. These biomimetic membrane systems feature unique structural flexibility and expandability and, unlike solid-state microfluidic and nanofluidic devices prepared by top-down fabrication, they allow network designs with dynamic control over individual containers and interconnecting conduits. The fabrication is founded on self-assembly of phospholipid molecules, followed by micromanipulation operations, such as membrane electroporation and microinjection, to effect shape transformations of the membrane and create a series of interconnected compartments. Size and geometry of the network can be chosen according to its desired function. Membrane composition is controlled mainly during the self-assembly step, whereas the interior contents of individual containers is defined through a sequence of microneedle injections. Networks cannot be fabricated with other currently available methods of giant unilamellar vesicle preparation (large unilamellar vesicle fusion or electroformation). Described in detail are also three transport modes, which are suitable for moving water-soluble or membrane-bound small molecules, polymers, DNA, proteins and nanoparticles within the networks. The fabrication protocol requires ∼90 min, provided all necessary preparations are made in advance. The transport studies require an additional 60-120 min, depending on the transport regime. © 2011 Nature America, Inc. All rights reserved.
Open Access
Mutation in TOR1AIP1 encoding LAP1B in a form of muscular dystrophy: A novel gene related to nuclear envelopathies
(Elsevier Ltd, 2014) Kayman-Kurekci G.; Talim, B.; Korkusuz P.; Sayar, N.; Sarioglu, T.; Oncel I.; Sharafi P.; Gundesli H.; Balci-Hayta, B.; Purali, N.; Serdaroglu-Oflazer P.; Topaloglu H.; Dincer P.
We performed genome-wide homozygosity mapping and mapped a novel myopathic phenotype to chromosomal region 1q25 in a consanguineous family with three affected individuals manifesting proximal and distal weakness and atrophy, rigid spine and contractures of the proximal and distal interphalangeal hand joints. Additionally, cardiomyopathy and respiratory involvement were noted. DNA sequencing of torsinA-interacting protein 1 (TOR1AIP1) gene encoding lamina-associated polypeptide 1B (LAP1B), showed a homozygous c.186delG mutation that causes a frameshift resulting in a premature stop codon (p.E62fsTer25). We observed that expression of LAP1B was absent in the patient skeletal muscle fibres. Ultrastructural examination showed intact sarcomeric organization but alterations of the nuclear envelope including nuclear fragmentation, chromatin bleb formation and naked chromatin. LAP1B is a type-2 integral membrane protein localized in the inner nuclear membrane that binds to both A- and B-type lamins, and is involved in the regulation of torsinA ATPase. Interestingly, luminal domain-like LAP1 (LULL1)-an endoplasmic reticulum-localized partner of torsinA-was overexpressed in the patient's muscle in the absence of LAP1B. Therefore, the findings suggest that LAP1 and LULL1 might have a compensatory effect on each other. This study expands the spectrum of genes associated with nuclear envelopathies and highlights the critical function for LAP1B in striated muscle. © 2014 Elsevier B.V.
Open Access
On the strain in silicon nanocrystals
(2009) Yılmaz, Dündar
In this Thesis we present our achievements towards an understanding of atomistic strain mechanisms and interface chemistry in silicon nanocrystals. The structural control of silicon nanocrystals embedded in amorphous oxide is currently an important technological problem. First, our initial attempt is described to simulate the structural behavior of silicon nanocrystals embedded in amorphous oxide matrix based on simple valence force fields as described by Keatingtype potentials. Next, the interface chemistry of silicon nanocrystals (NCs) embedded in amorphous oxide matrix is studied through molecular dynamics simulations with the chemical environment being governed by the reactive force field model. Our results indicate that the Si NC-oxide interface is more involved than the previously proposed schemes which were based on solely simple bridge or double bonds. We identify different types of three-coordinated oxygen complexes, previously not noted. The abundance and the charge distribution of each oxygen complex is determined as a function of the NC size as well as the transitions among them. Strain has a crucial effect on the optical and electronic properties of nanostructures. We calculate the atomistic strain distribution in silicon NCsup to a diameter of 3.2 nm embedded in an amorphous silicon dioxide matrix. A seemingly conflicting picture arises when the strain field is expressed in terms of bond lengths versus volumetric strain. The strain profile in either case shows uniform behavior in the core, however it becomes nonuniform within 2- 3 ˚A distance to the NC surface: tensile for bond lengths whereas compressive for volumetric strain. We reconcile their coexistence by an atomistic strain analysis. Vibrational density of states (VDOS) affects the optical properties of Si-NCs. VDOS obtained by calculating velocity autocorrelation function (VACF) using velocities of the atoms is extracted from the molecular dynamics simulations. The information on bonding topology enables classification of atoms in the system with respect to their neighbor atoms. With help of this information we separate contributions of different type of atoms to the VDOS. Calculating VACF of different type of atoms such as surface atoms and core atoms of nanocrystal, to the system facilitates understanding of the effects of strain fields and interface chemistry to the VDOS.
Open Access
Stratonovich-to-Itô transition in noisy systems with multiplicative feedback
(Nature Publishing Group, 2013) Pesce G.; McDaniel, A.; Hottovy, S.; Wehr J.; Volpe G.
Intrinsically noisy mechanisms drive most physical, biological and economic phenomena. Frequently, the system's state influences the driving noise intensity (multiplicative feedback). These phenomena are often modelled using stochastic differential equations, which can be interpreted according to various conventions (for example, Itô calculus and Stratonovich calculus), leading to qualitatively different solutions. Thus, a stochastic differential equation-convention pair must be determined from the available experimental data before being able to predict the system's behaviour under new conditions. Here we experimentally demonstrate that the convention for a given system may vary with the operational conditions: we show that a noisy electric circuit shifts from obeying Stratonovich calculus to obeying Itô calculus. We track such a transition to the underlying dynamics of the system and, in particular, to the ratio between the driving noise correlation time and the feedback delay time. We discuss possible implications of our conclusions, supported by numerics, for biology and economics. © 2013 Macmillan Publishers Limited. All rights reserved.
Open Access
Structures and free energy landscapes of the wild-type and A30P mutant-type α-synuclein proteins with dynamics
(2013) Wise-Scira O.; Aloglu, A.K.; Dunn, A.; Sakallioglu I.T.; Coskuner O.
The genetic missense A30P mutation of the wild-type α-synuclein protein results in the replacement of the 30th amino acid residue from alanine (Ala) to proline (Pro) and was initially found in the members of a German family who developed Parkinson's disease. Even though the structures of these proteins have been measured before, detailed understanding about the structures and their relationships with free energy landscapes is lacking, which is of interest to provide insights into the pathogenic mechanism of Parkinson's disease. We report the secondary and tertiary structures and conformational free energy landscapes of the wild-type and A30P mutant-type α-synuclein proteins in an aqueous solution environment via extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations. In addition, we present the residual secondary structure component transition stabilities at the atomic level with dynamics in terms of free energy change calculations using a new strategy that we reported most recently. Our studies yield new interesting results; for instance, we find that the A30P mutation has local as well as long-range effects on the structural properties of the wild-type α-synuclein protein. The helical content at Ala18-Gly31 is less prominent in comparison to the wild-type α-synuclein protein. The β-sheet structure abundance decreases in the N-terminal region upon A30P mutation of the wild-type α-synuclein, whereas the NAC and C-terminal regions possess larger tendencies for β-sheet structure formation. Long-range intramolecular protein interactions are less abundant upon A30P mutation, especially between the NAC and C-terminal regions, which is linked to the less compact and less stable structures of the A30P mutant-type rather than the wild-type α-synuclein protein. Results including the usage of our new strategy for secondary structure transition stabilities show that the A30P mutant-type α-synuclein tendency toward aggregation is higher than the wild-type α-synuclein but we also find that the C-terminal and NAC regions of the A30P mutant-type α-synuclein are reactive toward fibrillzation and aggregation based on atomic level studies with dynamics in an aqueous solution environment. Therefore, we propose that small molecules or drugs blocking the specific residues, which we report herein, located in the NAC- and C-terminal regions of the A30P mutant-type α-synuclein protein might help to reduce the toxicity of the A30P mutant-type α-synuclein protein. © 2013 American Chemical Society.
Open Access
Structures of the E46K mutant-type α-synuclein protein and impact of E46K mutation on the structures of the wild-type α-synuclein protein
(2013) Wise-Scira O.; Dunn, A.; Aloglu, A.K.; Sakallioglu I.T.; Coskuner O.
The E46K genetic missense mutation of the wild-type α-synuclein protein was recently identified in a family of Spanish origin with hereditary Parkinson's disease. Detailed understanding of the structures of the monomeric E46K mutant-type α-synuclein protein as well as the impact of the E46K missense mutation on the conformations and free energy landscapes of the wild-type α-synuclein are required for gaining insights into the pathogenic mechanism of Parkinson's disease. In this study, we use extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations to assess the secondary and tertiary structural properties as well as the conformational preferences of the monomeric wild-type and E46K mutant-type α-synuclein proteins in an aqueous solution environment. We also present the residual secondary structure component conversion stabilities with dynamics using a theoretical strategy, which we most recently developed. To the best of our knowledge, this study presents the first detailed comparison of the structural and thermodynamic properties of the wild-type and E46K mutant-type α-synuclein proteins in an aqueous solution environment at the atomic level with dynamics. We find that the E46K mutation results not only in local but also in long-range changes in the structural properties of the wild-type α-synuclein protein. The mutation site shows a significant decrease in helical content as well as a large increase in β-sheet structure formation upon E46K mutation. In addition, the β-sheet content of the C-terminal region increases significantly in the E46K mutant-type αS in comparison to the wild-type αS. Our theoretical strategy developed to assess the thermodynamic preference of secondary structure transitions indicates that this shift in secondary structure is the result of a decrease in the thermodynamic preference of turn to helix conversions while the coil to β-sheet preference increases for these residues. Long-range intramolecular protein interactions of the C-terminal with the N-terminal and NAC regions increase upon E46K mutation, resulting in more compact structures for the E46K mutant-type rather than wild-type αS. However, the E46K mutant-type αS structures are less stable than the wild-type αS. Overall, our results show that the E46K mutant-type αS has a higher propensity to aggregate than the wild-type αS and that the N-terminal and C-terminal regions are reactive toward fibrillization and aggregation upon E46K mutation and we explain the associated reasons based on the structural properties herein. Small molecules or drugs that can block the specific residues forming abundant β-sheet structure, which we report here, might help to reduce the reactivity of these intrinsically disordered fibrillogenic proteins toward aggregation and their toxicity. © 2013 American Chemical Society.