arXiv subjects

Walter Greiner

Publications and source records attributed to Walter Greiner.

At least 55 records · Page 3Linked to original sources

arXiv2007

MCHIT - Monte Carlo model for proton and heavy-ion therapy

We study the propagation of nucleons and nuclei in tissue-like media within a Monte Carlo Model for Heavy-ion Therapy (MCHIT) based on the GEANT4 toolkit (version 8.2). The model takes into account fragmentation of projectile nuclei and secondary interactions of produced nuclear fragments. Model predictions are validated with available experimental data obtained for water and PMMA phantoms irradiated by monoenergetic carbon-ion beams. The MCHIT model describes well (1) the depth-dose distributions in water and PMMA, (2) the doses measured for fragments of certain charge, (3) the distributions of positron emitting nuclear fragments produced by carbon-ion beams, and (4) the energy spectra of secondary neutrons measured at different angles to the beam direction. Radial dose profiles for primary nuclei and for different projectile fragments are calculated and discussed as possible input for evaluation of biological dose distributions. It is shown that at the periphery of the transverse dose profile close to the Bragg peak the dose from secondary nuclear fragments is comparable to the dose from primary nuclei.

physics.med-ph↗

arXiv2007

Alpha helix-coil phase transition: analysis of ab initio theory predictions

In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [1] and perform detail analysis of alpha helix-random coil transition in alanine polypeptides of different length. We have calculated the potential energy surfaces of polypeptides with respect to their twisting degrees of freedom and construct a parameter-free partition function of the polypeptide using the suggested method [1]. From the build up partition function we derive various thermodynamical characteristics for alanine polypeptides of different length as a function of temperature. Thus, we analyze the temperature dependence of the heat capacity, latent heat and helicity for alanine polypeptides consisting of 21, 30, 40, 50 and 100 amino acids. Alternatively, we have obtained same thermodynamical characteristics from the use of molecular dynamics simulations and compared them with the results of the new statistical mechanics approach. The comparison proves the validity of the statistical mechanic approach and establishes its accuracy.

physics.bio-ph↗

arXiv2007

Ab initio theory of helix-coil phase transition

In this paper we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix-random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory which is free of model parameters and is based solely on fundamental physical principles. It describes essential thermodynamical properties of the system such as heat capacity, the phase transition temperature and others from the analysis of the polypeptide potential energy surface calculated as a function of two dihedral angles, responsible for the polypeptide twisting. The suggested theory is general and with some modification can be applied for the description of phase transitions in other complex molecular systems (e.g. proteins, DNA, nanotubes, atomic clusters, fullerenes).

physics.bio-ph↗

arXiv2007

Comparative study of depth-dose distributions for beams of light and heavy nuclei in tissue-like media

We study the energy deposition by light and heavy nuclei in tissue-like media as used for cancer therapy. The depth-dose distributions for protons, $^{3}$He, $^{12}$C, $^{20}$Ne, and $^{58}$Ni nuclei are calculated within a Monte Carlo model based on the GEANT4 toolkit. These distributions are compared with each other and with available experimental data. It is demonstrated that nuclear fragmentation reactions essentially reduce the peak-to-plateau ratio of the dose profiles for deeply penetrating energetic ions heavier than $^{3}$He. On the other hand, all projectiles up to $^{20}$Ne were found equally suitable for therapeutic use at low penetration depths.

physics.med-ph↗

arXiv2007

Towards understanding of birds magnetoreceptor mechanism

In the present letter we suggest a new theoretical model for a quantitative description of the magnetoreception mechanism in birds. The considered mechanism involves two types of iron minerals (magnetite and maghemite) which were found in subcellular compartments within sensory dendrites of the upper beak of several bird species. The analysis of forces acting between the iron particles shows that the orientation of the external geomagnetic field can significantly change the probability of the mechanosensitive ion channels opening and closing. The performed theoretical analysis shows that the suggested magnetoreceptor system might be a sensitive biological magnetometer providing an essential part of the magnetic map for navigation.

physics.bio-ph↗

arXiv2007

Two center multipole expansion method: application to macromolecular systems

We propose a new theoretical method for the calculation of the interaction energy between macromolecular systems at large distances. The method provides a linear scaling of the computing time with the system size and is considered as an alternative to the well known fast multipole method. Its efficiency, accuracy and applicability to macromolecular systems is analyzed and discussed in detail.

physics.bio-ph↗

arXiv2007

Electron-based crystalline undulator

We discuss the features of a crystalline undulator of the novel type based on the effect of a planar channeling of ultra-relativistic electrons in a periodically bent crystals. It is demonstrated that an electron-based undulator is feasible in the tens of GeV range of the beam energies, which is noticeably higher than the energy interval allowed in a positron-based undulator. Numerical analysis of the main parameters of the undulator as well as the characteristics of the emitted undulator radiation is carried out for 20 and 50 GeV electrons channeling in diamond and silicon crystals along the (111) crystallographic planes.

physics.acc-ph↗

arXiv2006

Parameters of the crystalline undulator and its radiation for particular experimental conditions

We report the results of theoretical and numerical analysis of the crystalline undulators planned to be used in the experiments which are the part of the ongoing PECU project [1]. The goal of such an analysis was to define the parameters (different from those pre-set by the experimental setup) of the undulators which ensure the highest yield of photons of specified energies. The calculations were performed for 0.6 and 10 GeV positrons channeling through periodically bent Si and Si$_{1-x}$Ge$_x$ crystals.

physics.acc-ph↗

arXiv2006

Feasibility of an electron-based crystalline undulator

The feasibility to generate powerful monochromatic radiation of the undulator type in the gamma region of the spectrum by means of planar channeling of ultra-relativistic electrons in a periodically bent crystal is proven. It is shown that an electron-based crystalline undulator operates in the regime of higher beam energies than a positron-based one does. A numerical analysis is performed for a 50 GeV electron channeling in Si along the (111) crystallographic planes.

physics.acc-ph↗

arXiv2006

Distributions of positron-emitting nuclei in proton and carbon-ion therapy studied with GEANT4

Depth distributions of positron-emitting nuclei in PMMA phantoms are calculated within a Monte Carlo model for Heavy-Ion Therapy (MCHIT) based on the GEANT4 toolkit (version 8.0). The calculated total production rates of $^{11}$C, $^{10}$C and $^{15}$O nuclei are compared with experimental data and with corresponding results of the FLUKA and POSGEN codes. The distributions of e$^+$ annihilation points are obtained by simulating radioactive decay of unstable nuclei and transporting positrons in surrounding medium. A finite spatial resolution of the Positron Emission Tomography (PET) is taken into account in a simplified way. Depth distributions of $β^+$-activity as seen by a PET scanner are calculated and compared to available data for PMMA phantoms. The calculated $β^+$-activity profiles are in good agreement with PET data for proton and $^{12}$C beams at energies suitable for particle therapy. The MCHIT capability to predict the $β^+$-activity and dose distributions in tissue-like materials of different chemical composition is demonstrated.

physics.med-ph↗

arXiv2006

Neutron spin polarization in strong magnetic fields

The effects of strong magnetic fields on the inner crust of neutron stars are investigated after taking into account the anomalous magnetic moments of nucleons. Energy spectra and wave functions for protons and neutrons in a uniform magnetic field are provided. The particle spin polarizations and the yields of protons and neutrons are calculated in a free Fermi gas model. Obvious spin polarization occurs when $B\geq10^{14}$G for protons and $B\geq10^{17}$G for neutrons, respectively. It is shown that the neutron spin polarization depends solely on the magnetic field strength.

astro-ph↗

arXiv2005

Ab initio study of alanine polypeptide chains twisting

We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles Phi and Psi for alanine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.

physics.bio-ph↗

arXiv2005

Conformational changes in glycine tri- and hexapeptide

We have investigated the potential energy surfaces for glycine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of the characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles phi and psi for the glycine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.

physics.bio-ph↗

arXiv2005

Potential energy surfaces for cluster emitting nuclei

Potential energy surfaces are calculated by using the most advanced asymmetric two-center shell model allowing to obtain shell and pairing corrections which are added to the Yukawa-plus-exponential model deformation energy. Shell effects are of crucial importance for experimental observation of spontaneous disintegration by heavy ion emission. Results for 222Ra, 232U, 236Pu and 242Cm illustrate the main ideas and show for the first time for a cluster emitter a potential barrier obtained by using the macroscopic-microscopic method.

nucl-th↗

arXiv2005

Neutrons from fragmentation of light nuclei in tissue-like media: a study with GEANT4 toolkit

We study energy deposition by light nuclei in tissue-like media taking into account nuclear fragmentation reactions, in particular, production of secondary neutrons. The calculations are carried out within a Monte Carlo model for Heavy-Ion Therapy (MCHIT) based on the GEANT4 toolkit. Experimental data on depth-dose distributions for 135A-400A MeV C-12 and O-18 beams are described very well without any adjustment of the model parameters. This gives confidence in successful use of the GEANT4 toolkit for MC simulations of cancer therapy with beams of light nuclei. The energy deposition due to secondary neutrons produced by C-12 and Ne-20 beams in a (40-50 cm)^3 water phantom is estimated to 1-2% of the total dose, that is only slightly above the neutron contribution (~1%) induced by a 200 MeV proton beam.

physics.med-ph↗

arXiv2004

Rotating compact stars with exotic matter

We have constructed models of uniformly rotating compact stars including hyperons, Bose-Einstein condensates of antikaons and quarks. First order phase transitions from hadronic to antikaon condensed matter and then to quark matter are considered here. For the equation of state undergoing phase transitions to antikaon condensates, the third family of compact stars are found to exist in the fixed angular velocity sequences. However, the third family solution disappears when the compact stars rotate very fast. For this equation of state, the fixed baryon number supramassive sequence shows a second stable part after the unstable region but no back bending phenomenon. On the other hand, we observe that the rotation gives rise to a second maximum beyond the neutron star maximum for the equation of state involving phase transitions to both antikaon condensed and quark matter. In this case, the back bending phenomenon has been observed in the supramassive sequence as a consequence of the first order phase transition from $K^-$ condensed to quark matter. And the back bending segment contains stable configurations of neutron stars.

astro-ph↗

arXiv2004

Conformational properties of neutral and charged alanine and glycine chains

We have investigated the potential energy surface for neutral and charged alanine and glycine chains consisting of up to 6 amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi. Our calculations are performed within it ab initio theoretical framework based on the density functional theory and also within semi-empirical model approaches. We have demonstrated that the excessive positive charge of the system influences strongly its geometrical and conformational properties. With increasing of the excessive charge amino acid chains become unstable and decay into two or more fragments. We have analysed how the secondary structure of polypeptide chains influences the formation of the potential energy landscapes. We have calculated the energy barriers for transitions between different molecular conformations and determined the ones being energetically the most favourable.

physics.atm-clus↗

arXiv2004

Fission of charged alanine dipeptides

In this work we have performed for the first time a systematic analysis of the dissociation and fission pathways of neutral, singly and doubly charged alanine dipeptide ions with the aim to identify the fission mechanism and the most probable fragmentation channels of these type of molecules. We demonstrate the importance of rearrangement of the molecule structure during the fission process. This rearrangement may include transition to another isomer or a quasi-molecular state before actual separation of the daughter fragments begins.

physics.atm-clus↗