High-performance solution of hierarchical equations of motions for studying energy-transfer in light-harvesting complexes

Excitonic models of light-harvesting complexes, where the vibrational degrees of freedom are treated as a bath, are commonly used to describe the motion of the electronic excitation through a molecule. Recent experiments point toward the possibility of memory effects in this process and require to consider time non-local propagation techniques. The hierarchical equations of motion (HEOM) were proposed by Ishizaki and Fleming to describe the site-dependent reorganization dynamics of protein environments (J. Chem. Phys., 130, p. 234111, 2009), which plays a significant role in photosynthetic electronic energy transfer. HEOM are often used as a reference for other approximate methods, but have been implemented only for small systems due to their adverse computational scaling with the system size. Here, we show that HEOM are also solvable for larger systems, since the underlying algorithm is ideally suited for the usage of graphics processing units (GPU). The tremendous reduction in computational time due to the GPU allows us to perform a systematic study of the energy-transfer efficiency in the Fenna-Matthews-Olson (FMO) light-harvesting complex at physiological temperature under full consideration of memory-effects. We find that approximative methods differ qualitatively and quantitatively from the HEOM results and discuss the importance of finite temperature to achieve high energy-transfer efficiencies.Comment: 14 pages; Journal of Chemical Theory and Computation (2011

Quantum search algorithms

In this thesis two quantum search algorithms on two different graphs, a hypercube and a d-dimensional square lattice, are analysed and some applications of the lattice search are discussed. The approach in this thesis generalises a picture drawn by Shenvi, Kempe and Whaley, which was later adapted by Ambainis, Kempe and Rivosh. It defines a one parameter family of unitary operators U_λ with parameter λ. It will be shown that two eigenvalues of U_λ form an avoided crossing at the λ-value where U_λ is equal to the old search operator. This generalised picture opens the way for a construction of two approximate eigen- vectors at the crossing and gives rise to a 2×2 model Hamiltonian that is used to approximate the operator U_λ near the crossing. The thus defined Hamiltonian can be used to calculate the leading order of search time and success probability for the search. To the best of my knowledge only the scaling of these quantities has been known. For the algorithm searching the regular lattice, a generalisation of the model Hamiltonian for m target vertices is constructed. This algorithm can be used to send a signal from one vertex of the graph to a set of vertices. The signal is transmitted between these vertices exclusively and is localised only on the sender and the receiving vertices while the probability to measure the signal at one of the remaining vertices is significantly smaller. However, this effect can be used to introduce an additional sender to search settings and send a continuous signal to all target vertices where the signal will localise. This effect is an improvement compared to the original search algorithm as it does not need to know the number of target vertices

Quantum search algorithms

In this thesis two quantum search algorithms on two different graphs, a hypercube and a d-dimensional square lattice, are analysed and some applications of the lattice search are discussed. The approach in this thesis generalises a picture drawn by Shenvi, Kempe and Whaley, which was later adapted by Ambainis, Kempe and Rivosh. It defines a one parameter family of unitary operators U_λ with parameter λ. It will be shown that two eigenvalues of U_λ form an avoided crossing at the λ-value where U_λ is equal to the old search operator. This generalised picture opens the way for a construction of two approximate eigen- vectors at the crossing and gives rise to a 2×2 model Hamiltonian that is used to approximate the operator U_λ near the crossing. The thus defined Hamiltonian can be used to calculate the leading order of search time and success probability for the search. To the best of my knowledge only the scaling of these quantities has been known. For the algorithm searching the regular lattice, a generalisation of the model Hamiltonian for m target vertices is constructed. This algorithm can be used to send a signal from one vertex of the graph to a set of vertices. The signal is transmitted between these vertices exclusively and is localised only on the sender and the receiving vertices while the probability to measure the signal at one of the remaining vertices is significantly smaller. However, this effect can be used to introduce an additional sender to search settings and send a continuous signal to all target vertices where the signal will localise. This effect is an improvement compared to the original search algorithm as it does not need to know the number of target vertices

Quantum search algorithms on a regular lattice

Quantum algorithms for searching one or more marked items on a d-dimensional lattice provide an extension of Grover's search algorithm including a spatial component. We demonstrate that these lattice search algorithms can be viewed in terms of the level dynamics near an avoided crossing of a one-parameter family of quantum random walks. We give approximations for both the level-splitting at the avoided crossing and the effectively two-dimensional subspace of the full Hilbert space spanning the level crossing. This makes it possible to give the leading order behaviour for the search time and the localisation probability in the limit of large lattice size including the leading order coefficients. For d=2 and d=3, these coefficients are calculated explicitly. Closed form expressions are given for higher dimensions

Modelling of Oscillations in Two-Dimensional Echo-Spectra of the Fenna-Matthews-Olson Complex

Recent experimental observations of time-dependent beatings in the two-dimensional echo-spectra of light-harvesting complexes at ambient temperatures have opened up the question whether coherence and wave-like behaviour plays a significant role in photosynthesis. We perform a numerical study of the absorption and echo-spectra of the Fenna-Matthews-Olson (FMO) complex in chlorobium tepidum and analyse the requirements in the theoretical model needed to reproduce beatings in the calculated spectra. The energy transfer in the FMO pigment-protein complex is theoretically described by an exciton Hamiltonian coupled to a phonon bath which account for the pigments electronic and vibrational excitations respectively. We use the hierarchical equations of motions method to treat the strong couplings in a non-perturbative way. We show that the oscillations in the two-dimensional echo-spectra persist in the presence of thermal noise and static disorder.Comment: updated text and references, corrected figures 4-7, 20 pages, 7 figure

Dried blood spot analysis for the quantification of vancomycin and creatinine using liquid chromatography – tandem mass spectrometry:Method development and validation

Background: Vancomycin is a widely used antibiotic for the treatment of gram-positive bacterial infections, especially for methicillin-resistant Staphylococcus aureus (MRSA) infections. Due to a small therapeutic range and large inter-patient variability, therapeutic drug monitoring (TDM) of vancomycin is required to minimize toxicity and maximize treatment efficacy. Venous blood sampling is mostly applied for TDM of vancomycin, although this widely used sampling method is more invasive compared to less painful alternatives, such as the dried blood spot (DBS) method, which can be performed at home. Method: We developed an UPLC-MS/MS method for the quantification of vancomycin and creatinine in DBS. A fast sample preparation and short analysis run time of 5.2 min were applied, which makes this method highly suitable for clinical settings. Validation was performed according to international (FDA and EMA) guidelines. Results: The validated concentration range was found linear for creatinine from 41.8 µmol/L to 722 µmol/L and for vancomycin from 3.8 mg/L to 76.6 mg/L (r2 &gt; 0.990) and the inaccuracies, imprecisions, hematocrit effects, and recoveries were &lt; 15 % for both compounds. No significant carryover effect was observed. Conclusion: Hence, we successfully validated a quantification method for the simultaneous determination of creatinine and vancomycin in DBS.</p

Best practices, implementation and challenges of outpatient parenteral antimicrobial therapy:results of a worldwide survey among healthcare providers.

Background: Outpatient Parenteral Antimicrobial Therapy (OPAT) is considered a patient-friendly and cost-effective practice. Patients in the OPAT service can be at risk for developing adverse events. Due to extensive variations in practice, guidelines have been developed to minimize the risks. Objectives: In this first worldwide survey on OPAT, we explored the current OPAT services around the world, adherence to recommendations and identified best practices and challenges from different perspectives. Methods: An e-survey was conducted and consisted of questions about demographics, characteristics of the OPAT service, role of pharmacy, future developments, and respondents’ views on improvements as well as best practices. Results: A total of 126 responses from 28 countries were included. Seventy-eight percent (78%) of the respondents stated that their facility provides antimicrobial therapy in the outpatient setting, whereas 22% did not. Forty-two percent (42%) of the hospitals with OPAT services had a specialized OPAT service, while 14% lacked specialized services and 22% had a partially specialized team in place. In facilities with a specialized OPAT service, the number of mandatory infectious disease (ID) consultations before discharge and clinical monitoring by an ID specialist or OPAT team member, the frequency of monitoring, and the availability of an OPAT registry were higher. A multidisciplinary team’s presence was commonly noted as best practices. On the other hand, respondents experienced difficulties with reimbursement and lack of standardization in the screening, follow-up and monitoring of patients. Conclusion: This survey provides a better understanding of the implementation and practices of OPAT services globally and describes best practices and the challenges from different professionals.</p

Best practices, implementation and challenges of outpatient parenteral antimicrobial therapy:results of a worldwide survey among healthcare providers.

Background: Outpatient Parenteral Antimicrobial Therapy (OPAT) is considered a patient-friendly and cost-effective practice. Patients in the OPAT service can be at risk for developing adverse events. Due to extensive variations in practice, guidelines have been developed to minimize the risks. Objectives: In this first worldwide survey on OPAT, we explored the current OPAT services around the world, adherence to recommendations and identified best practices and challenges from different perspectives. Methods: An e-survey was conducted and consisted of questions about demographics, characteristics of the OPAT service, role of pharmacy, future developments, and respondents’ views on improvements as well as best practices. Results: A total of 126 responses from 28 countries were included. Seventy-eight percent (78%) of the respondents stated that their facility provides antimicrobial therapy in the outpatient setting, whereas 22% did not. Forty-two percent (42%) of the hospitals with OPAT services had a specialized OPAT service, while 14% lacked specialized services and 22% had a partially specialized team in place. In facilities with a specialized OPAT service, the number of mandatory infectious disease (ID) consultations before discharge and clinical monitoring by an ID specialist or OPAT team member, the frequency of monitoring, and the availability of an OPAT registry were higher. A multidisciplinary team’s presence was commonly noted as best practices. On the other hand, respondents experienced difficulties with reimbursement and lack of standardization in the screening, follow-up and monitoring of patients. Conclusion: This survey provides a better understanding of the implementation and practices of OPAT services globally and describes best practices and the challenges from different professionals.</p