scholarly journals First-principles design of nanomachines

2009 ◽  
Vol 106 (17) ◽  
pp. 6900-6903 ◽  
Author(s):  
Jayanth R. Banavar ◽  
Marek Cieplak ◽  
Trinh Xuan Hoang ◽  
Amos Maritan
Keyword(s):  
First Principles ◽  
Reference Frames ◽  
Hard Spheres ◽  
Molecular Machines ◽  
Thermal Fluctuations ◽  
Chain Molecule ◽  
Inherent Anisotropy ◽  
Predictive Design ◽  
Simple Chain ◽  
A Chain

Learning from nature's amazing molecular machines, globular proteins, we present a framework for the predictive design of nanomachines. We show that the crucial ingredients for a chain molecule to behave as a machine are its inherent anisotropy and the coupling between the local Frenet coordinate reference frames of nearby monomers. We demonstrate that, even in the absence of heterogeneity, protein-like behavior is obtained for a simple chain molecule made up of just 30 hard spheres. This chain spontaneously switches between 2 distinct geometries, a single helix and a dual helix, merely because of thermal fluctuations.

Influence of the solvent on the conformation of a chain molecule

1998 ◽  
Vol 109 (5) ◽  
pp. 2011-2022 ◽  
Author(s):  
Hin Hark Gan ◽  
Byung Chan Eu
Keyword(s):  
Chain Molecule ◽  
A Chain

scholarly journals Molecular machines operating on the nanoscale: from classical to quantum

2016 ◽  
Vol 7 ◽  
pp. 328-350 ◽  
Author(s):  
Igor Goychuk
Keyword(s):  
Molecular Motors ◽  
High Performance ◽  
Molecular Machines ◽  
Thermal Fluctuations ◽  
Maximum Power ◽  
Thermodynamic Efficiency ◽  
Fluctuation Dissipation ◽  
Fluctuation Dissipation Theorem ◽  
Physical Features

The main physical features and operating principles of isothermal nanomachines in the microworld, common to both classical and quantum machines, are reviewed. Special attention is paid to the dual, constructive role of dissipation and thermal fluctuations, the fluctuation–dissipation theorem, heat losses and free energy transduction, thermodynamic efficiency, and thermodynamic efficiency at maximum power. Several basic models are considered and discussed to highlight generic physical features. This work examines some common fallacies that continue to plague the literature. In particular, the erroneous beliefs that one should minimize friction and lower the temperature for high performance of Brownian machines, and that the thermodynamic efficiency at maximum power cannot exceed one-half are discussed. The emerging topic of anomalous molecular motors operating subdiffusively but very efficiently in the viscoelastic environment of living cells is also discussed.

Contribution of the Torsional Modes to the Equilibrium Distribution of Vibrational States and to the Specific Heat of a Chain Molecule

1983 ◽  
Vol 38 (12) ◽  
pp. 1285-1292 ◽  
Author(s):  
J. A. Borges da Costa ◽  
C. Scherer ◽  
A. Holz ◽  
J. Naghizadeh
Keyword(s):  
Specific Heat ◽  
Equilibrium Distribution ◽  
Spatial Configuration ◽  
Low Frequency ◽  
Chain Molecule ◽  
Vibrational States ◽  
Polymer Molecules ◽  
The Mean ◽  
A Chain ◽  
Increasing Temperature

Abstract The torsional modes of a chain molecule were studied recently under the assumption that it has a well defined spatial configuration at any time. Here we show how the averages over the possible configurations, for a distribution in thermal equilibrium, should be performed in the calculation of the thermodynamical properties. Our results show that the mean density of torsional states increases in the low frequency region with increasing temperature. The specific heat behaviour shows a considerable difference from the result obtained in the previous paper, where only the lowest energetic configuration was considered. The consequences of this result with respect to the configurational properties of polymer molecules near the θ temperature are discussed.

scholarly journals Boar proacrosin is a single-chain molecule which has the N-terminus of the acrosin A-chain (light chain)

FEBS Letters ◽  
1988 ◽  
Vol 241 (1-2) ◽  
pp. 136-140 ◽  
Author(s):  
D. Čechová ◽  
E. Töpfer-Petersen ◽  
A. Henschen
Keyword(s):  
Light Chain ◽  
Chain Molecule ◽  
Single Chain ◽  
N Terminus ◽  
A Chain

scholarly journals The torsional flexibility of aliphatic chain molecules

1940 ◽  
Vol 174 (956) ◽  
pp. 137-144 ◽  
Keyword(s):  
Room Temperature ◽  
Threshold Energy ◽  
Chain Molecule ◽  
Aliphatic Chain ◽  
Chain Molecules ◽  
Distortion Effect ◽  
A Chain ◽  
Single Bonds ◽  
Long Chain ◽  
Made In

The rotation of the CH 3 groups round the single C—C bond in ethane is associated with a threshold energy of about 3000 gcal./gmol. or 2 x 10 -13 erg/mol. (Schäfer 1938; Kistiakowsky, Lacher and Strutt 1939). In an aliphatic CH 2 chain where the carbon atoms are linked together by single bonds the corresponding energy must be of the same order and is most likely rather smaller. Supposing we consider any particular C—C bond in the chain and treat the two parts at each side of this bond as rigid rotators, then their kinetic energy would be 2 x 1/2 kT which at room temperature amounts to about one-fifth of the threshold energy. It seems very likely under these circumstances that a chain molecule of say ten to twenty carbon atoms should already at room temperature show signs of distortion due to internal rotation. If this is true, then the previously observed increase of the crystal symmetry at the melting-point of paraffins (Müller 1930, 1932) and the corresponding changes of the polarization of long-chain ketones (Müller 1937, 1938) can no longer be ascribed entirely to a rotation of the molecule in the field of the surrounding molecules but must at least partly be due to this internal distortion. It is clear that a distortion of this type tends to destroy the anisotropy of the molecule and to give an apparent isotropy to the crystal. The present experiments were made in order to obtain an estimate of the magnitude of the distortion effect. It is found to be surprisingly large.

Monte Carlo analysis of polymer translocation with deterministic and noisy electric fields

Open Physics ◽  
2012 ◽  
Vol 10 (3) ◽  
Author(s):  
Davide Valenti ◽  
Giovanni Denaro ◽  
Dominique Adorno ◽  
Nicola Pizzolato ◽  
Salvatore Zammito ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Electric Fields ◽  
Piecewise Linear ◽  
Biological Membrane ◽  
Monte Carlo Analysis ◽  
Chain Molecule ◽  
Electric Voltage ◽  
Polymer Translocation ◽  
Bond Fluctuation ◽  
A Chain

AbstractPolymer translocation through the nanochannel is studied by means of a Monte Carlo approach, in the presence of a static or oscillating external electric voltage. The polymer is described as a chain molecule according to the two-dimensional “bond fluctuation model”. It moves through a piecewise linear channel, which mimics a nanopore in a biological membrane. The monomers of the chain interact with the walls of the channel, modelled as a reflecting barrier. We analyze the polymer dynamics, concentrating on the translocation time through the channel, when an external electric field is applied. By introducing a source of coloured noise, we analyze the effect of correlated random fluctuations on the polymer translocation dynamics.

Correlation and Distribution of Segments in a Chain Molecule

1969 ◽  
Vol 51 (3) ◽  
pp. 1215-1221 ◽  
Author(s):  
Robert Yeh ◽  
A. Isihara
Keyword(s):  
Chain Molecule ◽  
A Chain

Molecular Cocrystals of Aromatic Carboxylic Acids with 1,1-Diethylurea: Synthesis and the Crystal Structures of a Series of Nitro-Substituted Analogues

2000 ◽  
Vol 53 (3) ◽  
pp. 203 ◽  
Author(s):  
Graham Smith ◽  
Michael G. Coyne ◽  
Jonathan M. White
Keyword(s):  
Hydrogen Bonding ◽  
Carboxylic Acids ◽  
Acid Group ◽  
X Ray Diffraction ◽  
Chain Polymer ◽  
Aromatic Carboxylic Acids ◽  
Nitrobenzoic Acid ◽  
Simple Chain ◽  
A Chain ◽  
Polymeric Structures

Molecular adducts of 1,1-diethylurea with the nitro-substituted aromatic carboxylic acids 2-nitrobenzoic acid, [(C7H5NO4)(C5H12N2O)] (1), 3-nitrobenzoic acid, [(C7H5NO4)(C5H12N2O)] (2), 4-nitrobenzoic acid, [(C7H5NO4)2(C5H12N2O)] (3), 3,5-dinitrobenzoic acid, [(C7H4N2O6)(C5H12N2O)] (4), 5-nitrosalicylic acid, [(C7H5NO5)(C5H12N2O)] (5) and 3,5-dinitrosalicylic acid, [(C7H4N2O7)(C5H12N2O)] (6), have been prepared and characterized by using infrared spectroscopy, and, in the case of four of these [(1), (4), (5) and (6)], by single-crystal X-ray diffraction methods. In all examples, primary cyclic hydrogen-bonding interactions are found between the amide group of the substituted urea and the carboxylic acid group of the acid, while further peripheral associations result predominantly in simple chain polymeric structures, and in one case [adduct (1)], a cyclic tetramer. The crystal structure of the parent 1,1-diethylurea has also been determined, revealing a cyclic hydrogen-bonded tetramer which forms into a chain polymer by weak hydrogen-bonding associations.

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