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Universität zu KölnFachgruppe PhysikTheoretische PhysikAG PortoMarkus Porto

Scientific interests

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In case you are interested in citations, etc., you might want to use my ResearcherID A-6546-2009.

Molecular biology and structural bioinformatics

Regular Articles in International Journals

(R30)
Lack of self-averaging in neutral evolution of proteins
U. Bastolla, M. Porto, H.E. Roman, and M. Vendruscolo, Phys. Rev. Lett. 89, 208101 (2002) (4 pages).
(R32)
Connectivity of neutral networks, overdispersion, and structural conservation in protein evolution
U. Bastolla, M. Porto, H.E. Roman, and M. Vendruscolo, J. Mol. Evol. 56, 243-254 (2003).
(R35)
Reconstruction of protein structures from a vectorial representation
M. Porto, U. Bastolla, H.E. Roman, and M. Vendruscolo, Phys. Rev. Lett. 92, 218101 (2004) (4 pages).
(R36)
Principal eigenvector of contact matrices and hydrophobicity profiles in proteins
U. Bastolla, M. Porto, H.E. Roman, and M. Vendruscolo, Proteins 58, 22-30 (2005).
(R37)
Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences
M. Porto, H.E. Roman, M. Vendruscolo, and U. Bastolla, Mol. Biol. Evol. 22, 630-638 (2005).
(R39)
A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank
U. Bastolla, M. Porto, H.E. Roman, and M. Vendruscolo, BMC Evol. Biol. 6, 43 (2006) (21 pages).
(R42)
Vectorial representation of single- and multi-domain protein folds
F. Teichert and M. Porto, Eur. Phys. J. B 54, 131-136 (2006).
(R45)
SABERTOOTH: Protein structural alignment based on a vectorial structure representation
F. Teichert, U. Bastolla, and M. Porto, BMC Bioinformatics 8, 425 (2007) (17 pages).
(R48)
Local interactions in protein folding determined through an inverse folding model
U. Bastolla, M. Porto, and A.R. Ortiz, Proteins 71, 278-299 (2008).
(R54)
Effective connectivity profile: A structural representation that evidences the relationship between protein structures and sequences
U. Bastolla, A.R. Ortiz, M. Porto, and F. Teichert, Proteins 73, 872-888 (2008).
(R55)
Stochastic reconstruction of protein structures from effective connectivity profiles
K. Wolff, M. Vendruscolo, and M. Porto, PMC Biophys. 1, 5 (2008) (13 pages).
(R59)
Efficient identification of near-native conformations in ab initio protein structure prediction using structural profiles
K. Wolff, M. Vendruscolo, and M. Porto, Proteins 78, 249-258 (2010).
(R60)
Mutation bias favors protein folding stability in the evolution of small populations
R. Méndez, M. Fritsche, M. Porto, and U. Bastolla, PLoS Comput. Biol. 6, e1000767 (2010) (21 pages).
(R61)
High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABERTOOTH
F. Teichert, J. Minning, U. Bastolla, and M. Porto, BMC Bioinformatics 11, 251 (2010) (14 pages).
(R62)
Comparison of translation loads for standard and alternative genetic codes
S.G. Sammet, U. Bastolla, and M. Porto, BMC Evol. Biol. 10, 178 (2010) (14 pages).
(R63)
Asymmetric folding pathways and transient misfolding in a coarse-grained model of proteins
K. Wolff, M. Vendruscolo, and M. Porto, EPL 94, 48005 (2011) (5 pages)
(R64)
Coarse-grained model for protein folding based on structural profiles
K. Wolff, M. Vendruscolo, and M. Porto, Phys. Rev. E 84, 041934 (2011) (7 pages).
(R66)
Detecting selection for negative design in proteins through an improved model of the misfolded state
J. Minning, M. Porto, and U. Bastolla, Proteins (in print).

Articles in Proceedings of Conferences in International Journals and Books

(P12)
Statistical properties of neutral evolution
U. Bastolla, M. Porto, H.E. Roman, and M. Vendruscolo, J. Mol. Evol. 57, S103-S119 (2003).
(International Conference `Molecular Evolution – Evolution, Genomics, Bioinformatics´, Sorrento, Italy, June 13 to 16, 2002)
(P13)
Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles
U. Bastolla, M. Porto, H.E. Roman, and M. Vendruscolo, Gene 347, 219-230 (2005).
(International Conference `Structural approaches to sequence evolution: Molecules, networks, populations´, Dresden, Germany, July 4 to 10, 2003)
(P15)
A stochastic method for the reconstruction of protein structures from one-dimensional structural profiles
K. Wolff, M. Vendruscolo, and M. Porto, Gene 422, 47-51 (2008).
(International Conference `Physical and chemical foundations of bioinformatics methods´, Dresden, Germany, June 18 to 22, 2007)
(P16)
Protein Structure Alignment through a Contact Topology Profile using SABERTOOTH
F. Teichert, U. Bastolla, and M. Porto, in German Conference on Bioinformatics – GCB 2008, edited by A. Beyer and M. Schroeder, Lecture Notes in Informatics No. P-136, Gesellschaft für Informatik e.V., Bonn, 2008, pp. 75-84.
(International Conference `German Conference on Bioinformatics 2008´, Dresden, Germany, September 9 to 12, 2008)

Invited and Contributed Review Chapters in Books

(C4)
The structurally constrained neutral model of protein evolution
U. Bastolla, M. Porto, H.E. Roman, and M. Vendruscolo, in Structural approaches to sequence evolution: Molecules, networks, populations, edited by U. Bastolla, M. Porto, H.E. Roman, and M. Vendruscolo, Springer, Berlin, 2007, pp. 75-113.
(C6)
Modeling structural and genomic constraints in the evolution of proteins
U. Bastolla and M. Porto, in Computational modeling of biological systems: From molecules to pathways, edited by N.V. Dokholyan, Springer, Berlin, 2012.

Edited Books and Edited Issues of International Journals

(E1)
Guest Editor of Gene for Issues 345(1) and 347(2)
together with U. Bastolla, H.E. Roman, and M. Vendruscolo.
(International Conference `Structural approaches to sequence evolution: Molecules, networks, populations´, Dresden, Germany, July 4 to 10, 2004).
(E2)
Structural approaches to sequence evolution: Molecules, networks, populations
U. Bastolla, M. Porto, H.E. Roman, and M. Vendruscolo, eds.
Springer Series `Biological and Medical Physics/Biomedical Engineering´, Springer, Berlin, Heidelberg, 2007.
(International Conference `Structural approaches to sequence evolution: Molecules, networks, populations´, Dresden, Germany, July 4 to 10, 2004).
(E3)
Guest Editor of Gene for Issue 422(1-2)
together with H.E. Roman and M. Vendruscolo.
(International Conference `Physical and chemical foundations of bioinformatics methods´, Dresden, Germany, June 18 to 22, 2007).
(E4)
Guest Editor of Proteomics for Issue 10(23)
together with H.E. Roman and M. Vendruscolo.
(International Conference `Physical principles of protein behavior in the cell´, Dresden, Germany, October 26 to 30, 2009).

Structure and dynamics of complex networks

Regular Articles in International Journals

(R40)
Multicomponent reaction-diffusion processes on complex networks
S. Weber and M. Porto, Phys. Rev. E 74, 046108 (2006) (8 pages).
(R44)
Generation of arbitrarily two-point correlated random networks
S. Weber and M. Porto, Phys. Rev. E 76, 046111 (2007) (9 pages).
(R47)
Generating random networks with given degree-degree correlations and degree-dependent clustering
A. Pusch, S. Weber, and M. Porto, Phys. Rev. E 77, 017101 (2008) (4 pages).
(R49)
Impact of Topology on the Dynamical Organization of Cooperation in the Prisoner's Dilemma Game
A. Pusch, S. Weber, and M. Porto, Phys. Rev. E 77, 036120 (2008) (6 pages).
(R50)
Pattern formation and efficiency of reaction-diffusion processes on complex networks
S. Weber, M.-Th. Hütt, and M. Porto, EPL 82, 28003 (2008) (5 pages).
(R57)
Efficiency based strategy spreading in the prisoner's dilemma game
S. Weber and M. Porto, Eur. Phys. J. B 69, 559-603 (2009).
(R65)
Network evolution towards optimal dynamical performance
S. Karalus and M. Porto, EPL 99, 38002 (2012) (5 pages).

Analysis and modeling of stochastic processes

Regular Articles in International Journals

(R3)
Structural and dynamical properties of the percolation backbone in two and three dimensions
M. Porto, A. Bunde, S. Havlin, and H.E. Roman, Phys. Rev. E 56, 1667-1675 (1997).
(R5)
Probability distribution of the shortest path on the percolation cluster, its backbone, and skeleton
M. Porto, S. Havlin, H.E. Roman, and A. Bunde, Phys. Rev. E (Rapid Comm.) 58, R5205-R5208 (1998).
(R15)
Critical packing fraction of rectangular particles on the square lattice
M. Porto and H.E. Roman, Phys. Rev. E 62, 100-102 (2000).
(R20)
Self-generated power-law tails in probability distributions
H.E. Roman and M. Porto, Phys. Rev. E 63, 036128 (2001) (4 pages).
(R21)
Anomalous scaling of stock price dynamics within ARCH-models
H.E. Roman, M. Porto, and N. Giovanardi, Eur. Phys. J. B (Rapid Note) 21, 155-158 (2001).
(R27)
Autoregressive processes with exponentially decaying probability distribution functions: Applications to daily variations of a stock market index
M. Porto and H.E. Roman, Phys. Rev. E 65, 046149 (2002) (6 pages).
(R34)
Autoregressive processes with anomalous scaling behavior: Applications to high-frequency variations of a stock market index
C. Dose, M. Porto, and H.E. Roman, Phys. Rev. E 67, 067103 (2003) (4 pages).
(R51)
Fractional derivatives of random walks: Time series with long-time memory
H.E. Roman and M. Porto, Phys. Rev. E 78, 031127 (2008) (10 pages).
(R52)
Fractional brownian motion with stochastic variance: Modeling absolute returns in stock markets
H.E. Roman and M. Porto, Int. J. Mod. Phys. C 19, 1221-1242 (2008).
(R53)
Skewness, long-time memory, and non-stationarity: Application to leverage effect in financial time series
H.E. Roman M. Porto, and C. Dose, EPL 84, 28001 (2008) (5 pages).
(R56)
Fluctuations of company yearly profits versus scaled revenue: Fat tail distribution of Lévy type
H.E. Roman, R.A. Siliprandi, C. Dose, C. Riccardi, and M. Porto, EPL 84, 68003 (2008) (6 pages).
(R58)
Long-time correlations in company profit fluctuations: Presence of extreme events
H.E. Roman, R.A. Siliprandi, C. Dose, and M. Porto, Phys. Rev. E 80, 036114 (2009) (7 pages).

Articles in Proceedings of Conferences in International Journals and Books

(P2)
Physik auf fraktalen Strukturen
A. Bunde, M. Porto, and H.E. Roman, in Fraktale im Unterricht – Zur didaktischen Bedeutung des Fraktalbegriffs, edited by M. Komorek, M. Schnegelberger, and R. Duit, Materialien des Instituts für Pädagogik der Naturwissenschaften (IPN), Kiel 1998, pp. 255-273.
(IPN Symposium on `Didaktik des Fraktalbegriffs´, Kiel, Germany, December 1996)
(P3)
Distribution of dangling ends of the incipient percolation cluster
M. Porto, A. Bunde, and S. Havlin, Physica A 266, 96-99 (1999).
(International Conference `Percolation and Disordered Systems´, Rauischholzhausen, Germany, July 14 to 17, 1998)
(P10)
Asset-asset interactions and clustering in financial markets
G. Cuniberti, M. Porto, and H.E. Roman, Physica A 299, 262-267 (2001).
(NATO Advanced Research Workshop on `Application of Physics in Economic Modelling´, Prague, Czech Republic, February 8 to 10, 2001)
(P14)
Very slowly decaying auto-correlations: Application to volatility in financial markets
H.E. Roman and M. Porto, International Journal of Pure and Applied Mathematics 42, 249-254 (2008).
(International Conference `Fourth International Conference of Applied Mathematics and Computing´, Plovdiv, Bulgaria, August 12 to 18, 2007)

Invited and Contributed Review Chapters in Books

(C1)
Random walks on fractals
A. Bunde, J. Dräger, and M. Porto, in Computational Physics: Selected Methods – Simple Exercises – Serious Applications, edited by K.H. Hoffmann and M. Schreiber, Springer, Berlin, Heidelberg, 1996, pp. 121-146.
(C5)
Long-time correlations and anomalous price fluctuations in stock markets
M. Porto and H.E. Roman, in Anomalous Fluctuations in Complex Systems: Plasmas, Fluids and Financial Markets, edited by C. Riccardi and H.E. Roman, Transworld Research Network, Kerala, 2007, pp. 335-354.

Interplay of disorder and long-range interaction

Regular Articles in International Journals

(R6)
Influence of the cubic anisotropy constants on the hysteresis loops of single-domain particles: A Monte Carlo study
J. García-Otero, M. Porto, J. Rivas, and A. Bunde, J. Appl. Phys. 85, 2287-2292 (1999).
(R8)
The influence of dipolar interaction on magnetic properties of ultrafine ferromagnetic particles
J. García-Otero, M. Porto, J. Rivas, and A. Bunde, Phys. Rev. Lett. 84, 167-170 (2000).
(R9)
Hopping transport in the presence of site energy disorder: Temperature and concentration scaling of conductivity spectra
M. Porto, P. Maass, M. Meyer, A. Bunde, and W. Dieterich, Phys. Rev. B 61, 6057-6062 (2000).
(R12)
On the Henkel plots of single-domain ferromagnetic particles
J. García-Otero, M. Porto, and J. Rivas, J. Appl. Phys. 87, 7376-7381 (2000).
(R17)
Ewald summation of electrostatic interactions of systems with finite extent in two of three dimensions
M. Porto, J. Phys. A: Math. Gen. 33, 6211-6218 (2000).
(R26)
Effect of positional disorder in systems of ultrafine ferromagnetic particles
M. Porto, Eur. Phys. J. B 26, 229-234 (2002).
(R31)
Relative significance of particle anisotropy in systems of ultrafine ferromagnetic particles
M. Porto, J. Appl. Phys. 92, 6057-6061 (2002).
(R38)
Ordered systems of ultrafine ferromagnetic particles
M. Porto, Eur. Phys. J. B 45, 369-375 (2005).

Articles in Proceedings of Conferences in International Journals and Books

(P5)
Monte Carlo simulation of hysteresis loops of single-domain particles with cubic anisotropy and their temperature dependence
J. García-Otero, M. Porto, J. Rivas, and A. Bunde, J. Magn. Magn. Mater. 203, 268-270 (1999).
(International Conference on `Magnetism of Nanostructured Phases´, San Sebastian, Spain, September 4 to 6, 1998)

Polymers and optimal paths in disordered media

Regular Articles in International Journals

(R1)
Are branched polymers in the universality class of percolation?
A. Bunde, S. Havlin, and M. Porto, Phys. Rev. Lett. 74, 2714-2716 (1995).
(R2)
Branched polymers in the presence of impurities
M. Porto, A. Shehter, A. Bunde, and S. Havlin, Phys. Rev. E 54, 1742-1748 (1996).
(R4)
Optimal path in strong disorder and shortest path in invasion percolation with trapping
M. Porto, S. Havlin, S. Schwarzer, and A. Bunde, Phys. Rev. Lett. 79, 4060-4062 (1997).
(R7)
Optimal paths in disordered media: Scaling of the crossover from self-similar to self-affine behavior
M. Porto, N. Schwartz, S. Havlin, and A. Bunde, Phys. Rev. E (Rapid Comm.) 60, R2448-R2451 (1999).
(R13)
Multifractal behavior of linear polymers in disordered media
A. Ordemann, M. Porto, H.E. Roman, S. Havlin, and A. Bunde, Phys. Rev. E 61, 6858-6865 (2000).
(R18)
`Generalized des Cloizeaux´ exponent for self-avoiding walks on the incipient percolation cluster
A. Ordemann, M. Porto, H.E. Roman, and S. Havlin, Phys. Rev. E (Rapid Comm.) 63, 020104(R) (2001) (4 pages).
(R24)
Self-avoiding walks on Sierpinski lattices in two and three dimensions
A. Ordemann, M. Porto, and H.E. Roman, Phys. Rev. E 65, 021107 (2002) (6 pages).
(R29)
Self-avoiding walks on self-similar structures: Finite versus infinite ramification
A. Ordemann, M. Porto, and H.E. Roman, J. Phys. A: Math. Gen. 35, 8029-8041 (2002).
(R41)
Violation of the des Cloizeaux relation for self-avoiding walks on Sierpinski square lattices
F. Marini, A. Ordemann, M. Porto, and H.E. Roman, Phys. Rev. E 74, 051102 (2006) (5 pages).
(R46)
Temperature-dependent structural behavior of self-avoiding walks on Sierpinski carpets
M. Fritsche, H.E. Roman, and M. Porto, Phys. Rev. E 76, 061101 (2007) (5 pages).

Articles in Proceedings of Conferences in International Journals and Books

(P1)
Structure of self-avoiding walks on percolation clusters at criticality
H.E. Roman, A. Ordemann, M. Porto, A. Bunde, and S. Havlin, Phil. Mag. B 77, 1357-1371 (1998).
(International Minerva Workshop on `Mesoscopics, Fractals, and Neural Networks´, Eilat, Israel, March 25 to 27, 1997)
(P4)
Optimal path in weak and strong disorder
N. Schwartz, M. Porto, S. Havlin, and A. Bunde, Physica A 266, 317-321 (1999).
(International Conference `Percolation and Disordered Systems´, Rauischholzhausen, Germany, July 14 to 17, 1998)

Invited and Contributed Review Chapters in Books

(C3)
Self-avoiding walks on deterministic and random fractals: Numerical results (Invited Chapter)
A. Ordemann, H.E. Roman, and M. Porto, in Statistics of Linear Polymers in Disordered Media, edited by B.K. Chakrabarti, Elsevier, Amsterdam, London, 2005, pp. 195-233.

Machines on mesoscopic and molecular scales

Regular Articles in International Journals

(R14)
Atomic scale engines: Cars and wheels
M. Porto, M. Urbakh, and J. Klafter, Phys. Rev. Lett. 84, 6058-6061 (2000).
(Covered by Physics News Update No. 490 of June 22, 2000, and Nature Science Update of July 3, 2000)
(R16)
Molecular motor that never steps backwards
M. Porto, M. Urbakh, and J. Klafter, Phys. Rev. Lett. 85, 491-495 (2000).
(R19)
Molecular motor based entirely on the Coulomb interaction
M. Porto, Phys. Rev. E (Rapid Comm.) 63, 030102(R) (2001) (4 pages).
(R22)
Rectification by hopping motion through nonsymmetric potentials: Local versus global bias
M. Porto, Phys. Rev. E 64, 021109 (2001) (4 pages).
(R23)
Hopping motion of interacting particles: From time dependent interaction to directed transport
M. Porto, M. Urbakh, and J. Klafter, Phys. Rev. E 65, 011108 (2002) (6 pages).
(R25)
Directed transport of an asymmetric particle pair induced by non-equilibrium conditions
M. Porto, Eur. Phys. J. B 25, 345-350 (2002).
(R43)
Mesoscale engines by nonlinear friction
D. Fleishman, J. Klafter, M. Porto, and M. Urbakh, Nano Lett. 7, 837-842 (2007).

Articles in Proceedings of Conferences in International Journals and Books

(P8)
Atomic scale engines: Taking a turn
M. Porto, M. Urbakh, and J. Klafter, Acta Phys. Pol. B 32, 295-306 (2001).
(XXIV International School of Theoretical Physics `Transport Phenomena from Quantum to Classical Regimes´, Ustron, Poland, September 25 to October 1, 2000)
(P11)
Motors on the molecular scale
M. Porto, M. Urbakh, and J. Klafter, J. Luminescence 94-95, 137-142 (2001).
(International Conference on `Dynamical Processes in Excited States of Solids´, Lyon, France, July 1 to 4, 2001)

Electron transport in mesoscopic and molecular systems

Regular Articles in International Journals

(R28)
Pure-carbon ring transistor: Role of topology and structure
G. Cuniberti, J. Yi, and M. Porto, Appl. Phys. Lett. 81, 850-852 (2002).
(R33)
Transmittance anomalies of a ring with lead-positional asymmetry
J. Yi, G. Cuniberti, and M. Porto, Eur. Phys. J. B 33, 221-225 (2003).

Invited and Contributed Review Chapters in Books

(C2)
Modeling of carbon-based nanojunctions (Invited Chapter)
J. Yi, G. Cuniberti, and M. Porto, in Encyclopedia of Nanoscience and Nanotechnology, edited by H.S. Nalwa, American Scientific Publishers, 2004, vol. 5, pp. 607-617.

Nanoscale friction

Regular Articles in International Journals

(R10)
Looking at friction through `shearons´
M. Porto, M. Urbakh, and J. Klafter, J. Phys. Chem. 104, 3791-3794 (2000).
(Cover story of this `Harvey Scher Festschrift´)
(R11)
Embedded systems under shear: Relationship between shear-induced modes and frictional behavior
M. Porto, M. Urbakh, and J. Klafter, Europhys. Lett. 50, 326-332 (2000).

Articles in Proceedings of Conferences in International Journals and Books

(P6)
Macroscopic versus Microscopic Description of Friction: From Tomlinson Model to Shearons
M. Porto, V. Zaloj, M. Urbakh, and J. Klafter, Trib. Lett. 9, 45-54 (2000).
(International Conference `Nanotribology: Theory, Experiment, Applications´, Ubud, Bali, April 11 to 14, 2000)
(P7)
Atomic scale friction: From basic characteristics to control
M. Porto, M. Urbakh, and J. Klafter, in Interfacial Properties on the Submicron Scale, edited by J.E. Frommer and R.M. Overney, ACS Symposium Series No. 781, American Chemical Society, Washington, DC, 2001, pp. 94-112.
(Session `Interfacial Properties on the Submicron Scale´ at the Fall 1999 Meeting of the American Chemical Society, New Orleans, USA, August 22 to 26, 1999)
(P9)
Towards a Microscopic Description of Friction
M. Porto, V. Zaloj, M. Urbakh, and J. Klafter, in Dynamics in Small Confining Systems V, edited by J.M. Drake, J. Klafter, P. Levitz, R.M. Overney, and M. Urbakh, MRS Symposium Proceedings No. 651, Materials Research Society, Pittsburgh, 2001, pp. T4.3.1-T4.3.12.
(Session `Dynamics in Small Confining Systems VI´ at the Fall 2000 Meeting of the Materials Research Society, Boston, USA, November 26 to December 1, 2000)