diff --git a/ionerdss/nerdss_analysis/data_readers.py b/ionerdss/nerdss_analysis/data_readers.py
index 74e492b0..acf2f349 100644
--- a/ionerdss/nerdss_analysis/data_readers.py
+++ b/ionerdss/nerdss_analysis/data_readers.py
@@ -341,14 +341,17 @@ class DataIO:
     def __init__(self):
         """
         Initialize a cache for storing data to avoid repeated file reads.
+        Also initialize last-modified time storage for cache invalidation.
         """
         self._cache = {}
+        self._modified = {}
         
     def clear_cache(self):
         """
         Clear the cached data.
         """
         self._cache = {}
+        self._modified = {}
         
     def get_copy_numbers(self, sim_dir: str) -> Optional[pd.DataFrame]:
         """
@@ -361,12 +364,19 @@ def get_copy_numbers(self, sim_dir: str) -> Optional[pd.DataFrame]:
             Optional[pd.DataFrame]: DataFrame containing the data, or None if file not found
         """
         cache_key = (sim_dir, "copy_numbers")
+        data_file = os.path.join(sim_dir, "DATA", "copy_numbers_time.dat")
+        mod_time = os.path.getmtime(data_file) # get last modified timestamp
+        
         if cache_key in self._cache:
-            return self._cache[cache_key]
+            if self._modified[cache_key] == mod_time:
+                return self._cache[cache_key]
+            else:
+                print("File modified, reloading from disk.")
         
         result = read_copy_numbers(sim_dir)
         if result is not None:
             self._cache[cache_key] = result
+            self._modified[cache_key] = mod_time
         return result
     
     def get_histogram_complexes(self, sim_dir: str) -> Dict[str, Any]:
@@ -380,11 +390,18 @@ def get_histogram_complexes(self, sim_dir: str) -> Dict[str, Any]:
             Dict[str, Any]: Dictionary containing time series and complex data
         """
         cache_key = (sim_dir, "histogram_complexes")
+        data_file = os.path.join(sim_dir, "DATA", "histogram_complexes_time.dat")
+        mod_time = os.path.getmtime(data_file) # get last modified timestamp
+        
         if cache_key in self._cache:
-            return self._cache[cache_key]
+            if self._modified[cache_key] == mod_time:
+                return self._cache[cache_key]
+            else:
+                print("File modified, reloading from disk.")
         
         result = read_histogram_complexes(sim_dir)
         self._cache[cache_key] = result
+        self._modified[cache_key] = mod_time
         return result
     
     def get_transition_matrix(self, sim_dir: str, time_frame: Optional[Tuple[float, float]] = None) -> Tuple[Optional[np.ndarray], Optional[Dict[int, List[float]]]]:
@@ -405,13 +422,19 @@ def get_transition_matrix(self, sim_dir: str, time_frame: Optional[Tuple[float,
         if time_frame is not None:
             time_str = f"{time_frame[0]}-{time_frame[1]}"
         cache_key = (sim_dir, "transition_matrix", time_str)
+        data_file = os.path.join(sim_dir, "DATA", "transition_matrix_time.dat")
+        mod_time = os.path.getmtime(data_file) # get last modified timestamp
         
         if cache_key in self._cache:
-            return self._cache[cache_key]
+            if self._modified[cache_key] == mod_time:
+                return self._cache[cache_key]
+            else:
+                print("File modified, reloading from disk.")
         
         result = read_transition_matrix(sim_dir, time_frame)
         if result[0] is not None:
             self._cache[cache_key] = result
+            self._modified[cache_key] = mod_time
         return result
     
     def get_multiple_copy_numbers(self, sim_dirs: List[str]) -> List[Optional[pd.DataFrame]]:
@@ -450,4 +473,4 @@ def get_multiple_transition_matrices(self, sim_dirs: List[str], time_frame: Opti
             List[Tuple[Optional[np.ndarray], Optional[Dict[int, List[float]]]]]: 
                 List of tuples containing transition matrix and lifetime data
         """
-        return [self.get_transition_matrix(sim_dir, time_frame) for sim_dir in sim_dirs]
\ No newline at end of file
+        return [self.get_transition_matrix(sim_dir, time_frame) for sim_dir in sim_dirs]